Contacts of the helix formed by residues 94 - 117 (chain A) in PDB entry 2F93
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLY 3.9 0.6 + - - +
93A LEU* 1.3 74.8 - - - +
95A SER* 1.3 65.5 + - - +
96A ARG* 3.1 11.7 + - - +
97A GLU* 2.8 46.8 + - - +
98A PHE* 3.0 22.5 + - - -
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP* 1.3 73.0 - - - +
96A ARG* 1.3 57.7 + - - +
98A PHE* 3.2 10.5 + - - +
99A GLY* 2.9 26.9 + - - -
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP* 3.1 11.4 + - - +
95A SER* 1.3 77.0 - - - +
97A GLU* 1.3 67.3 + - + +
99A GLY* 3.1 5.0 + - - -
100A ILE* 3.1 49.9 + - + +
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLY 4.4 1.4 - - - +
93A LEU* 3.3 32.3 - - + +
94A ASP* 2.8 46.8 + - - +
96A ARG* 1.3 76.4 - - + +
98A PHE* 1.3 66.4 + - - +
100A ILE* 3.3 14.0 + - + +
101A VAL* 3.3 26.0 + - - +
140A TYR* 5.8 1.5 - - + -
144A PRO* 6.1 1.0 - - - +
148A SER* 4.9 6.4 + - - -
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL 5.0 0.2 - - - -
85A TYR* 3.6 40.4 - + - -
88A GLY* 3.4 41.1 - - - -
89A LEU* 3.6 15.7 - - + -
93A LEU* 3.4 28.4 - - + +
94A ASP 3.0 23.7 + - - -
95A SER* 3.5 11.0 - - - +
97A GLU* 1.3 76.0 - - - +
99A GLY* 1.3 63.8 + - - +
101A VAL* 3.3 9.3 - - + +
102A ILE* 3.0 37.2 + - + +
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER 2.9 14.3 + - - -
96A ARG* 3.1 5.8 + - - -
98A PHE* 1.3 78.0 - - - +
100A ILE* 1.3 56.3 + - - +
102A ILE* 4.1 4.6 - - - +
103A THR* 2.7 34.6 + - - -
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG* 3.1 50.8 + - + +
97A GLU* 3.6 15.5 - - + +
98A PHE 3.2 0.4 - - - -
99A GLY* 1.3 77.0 - - - +
101A VAL* 1.3 60.0 + - - +
103A THR* 3.3 6.2 + - - -
104A LEU* 3.0 34.0 + - + +
140A TYR* 3.5 49.8 - - + +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 3.6 27.0 - - + +
93A LEU* 4.2 10.5 - - + -
97A GLU 3.3 12.3 + - - +
98A PHE* 3.3 17.3 - - + +
100A ILE* 1.3 74.1 - - - +
102A ILE* 1.3 65.6 + - + +
104A LEU* 3.8 5.8 - - - +
105A ASN* 2.9 30.3 + - - +
137A LEU* 4.0 11.5 - - + +
140A TYR* 3.7 31.4 - - + -
145A MET* 3.7 23.6 - - + -
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 3.5 39.3 - - + +
84A VAL* 4.1 15.5 - - + -
85A TYR* 4.5 8.7 - - + +
98A PHE* 3.0 32.2 + - + +
99A GLY* 4.1 4.3 - - - +
101A VAL* 1.3 75.4 - - + +
103A THR* 1.3 61.9 + - - +
105A ASN* 3.4 2.7 + - - +
106A THR* 2.8 44.0 + - - +
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Residues in contact with THR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLY 2.7 23.9 + - - -
100A ILE* 3.5 6.3 - - - -
101A VAL 3.2 0.2 - - - -
102A ILE* 1.3 75.4 - - - +
104A LEU* 1.3 70.0 + - + +
106A THR* 3.2 7.6 + - - -
107A VAL* 3.1 31.0 + - + +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE* 3.0 26.9 + - + +
101A VAL* 3.8 5.4 - - - +
103A THR* 1.3 79.4 - - + +
105A ASN* 1.3 63.0 + - - +
107A VAL* 3.2 17.7 + - + +
108A VAL* 3.2 18.1 + - - +
133A ALA* 3.8 24.1 - - + +
136A GLY* 3.8 18.4 - - - -
137A LEU* 3.9 9.6 - - + +
140A TYR* 3.5 38.1 - - + -
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Residues in contact with ASN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE 5.1 0.5 - - - +
80A THR* 2.9 25.2 + - - -
81A PRO* 3.5 18.4 - - + +
84A VAL* 3.6 15.9 - - + +
101A VAL 2.9 19.4 + - - +
102A ILE* 3.7 6.5 - - - +
104A LEU* 1.3 77.0 - - - +
106A THR* 1.3 65.3 + - - +
108A VAL* 3.2 7.3 + - - +
109A MET* 3.1 25.9 + - - +
137A LEU* 3.8 14.5 - - + +
171A TRP* 3.3 35.6 - - - -
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Residues in contact with THR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 5.5 11.9 + - + -
81A PRO* 5.1 4.3 - - - +
102A ILE* 2.8 30.4 + - - +
103A THR* 3.2 7.2 + - - -
105A ASN* 1.3 80.9 + - - +
107A VAL* 1.3 57.0 + - + +
109A MET* 3.3 4.4 + - - +
110A LEU* 2.9 53.8 + - + +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A THR* 3.1 24.3 + - + +
104A LEU* 3.2 10.3 + - + +
106A THR* 1.3 77.3 - - + +
108A VAL* 1.3 65.4 + - - +
110A LEU* 4.1 6.0 - - + +
111A ALA* 2.9 27.4 + - - +
129A MET* 3.7 34.2 - - + +
133A ALA* 3.6 19.3 - - + -
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU 3.2 14.6 + - - +
105A ASN* 3.2 10.3 + - - +
107A VAL* 1.3 78.5 - - - +
109A MET* 1.3 76.5 + - + +
111A ALA* 3.3 2.9 + - - +
112A GLY 3.1 18.2 + - - -
130A GLY* 3.4 12.0 - - - +
133A ALA* 3.6 2.2 - - + +
134A PHE* 3.3 41.3 - - + +
137A LEU* 5.1 3.6 - - + -
301A RET 3.7 46.7 - - + +
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Residues in contact with MET 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 5.1 2.6 - - - +
76A TRP* 3.9 24.1 - - + +
77A ILE* 3.7 27.4 - - + +
80A THR* 3.2 34.5 - - + +
105A ASN* 3.1 29.4 + - - +
106A THR* 3.9 4.7 - - - +
107A VAL 3.3 0.2 - - - -
108A VAL* 1.3 96.4 - - + +
110A LEU* 1.3 65.1 + - - +
112A GLY* 3.4 1.2 + - - -
113A PHE* 3.1 23.4 + - - +
137A LEU* 5.8 0.2 - - + -
171A TRP* 4.1 3.4 - - + -
301A RET 3.8 38.9 - - + +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE* 3.8 28.7 - - + -
106A THR* 2.9 44.0 + - + +
107A VAL* 4.1 4.9 - - + +
109A MET* 1.3 72.5 - - - +
111A ALA* 1.3 57.7 + - - +
113A PHE* 3.3 10.1 + - + +
114A ALA* 2.9 32.6 + - - +
129A MET* 5.3 4.5 - - + -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL 2.9 20.4 + - - +
108A VAL 3.4 5.2 - - - +
110A LEU* 1.3 77.8 - - - +
112A GLY* 1.3 56.9 + - - +
114A ALA* 4.7 3.1 - - - -
115A GLY* 2.8 29.1 + - - -
126A LEU* 3.3 30.9 - - - +
127A PHE 4.8 0.7 + - - -
129A MET* 3.7 17.9 - - + +
130A GLY* 3.5 16.2 - - - +
301A RET 5.1 0.9 - - + -
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 4.0 6.8 - - - -
108A VAL 3.1 11.1 + - - -
109A MET 3.4 0.6 + - - -
111A ALA* 1.3 76.1 - - - +
113A PHE* 1.3 56.8 + - - +
116A ALA* 3.0 30.7 + - - +
178A TRP* 3.2 12.1 + - - -
301A RET 3.5 35.6 - - - +
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Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA* 4.5 17.7 - - + -
73A TYR* 3.4 36.0 - + + -
74A ILE* 3.7 26.9 - - + -
77A ILE* 4.0 17.5 - - + -
109A MET 3.1 17.4 + - - +
110A LEU* 3.5 10.8 - - + +
111A ALA 3.2 0.2 - - - -
112A GLY* 1.3 74.3 - - - +
114A ALA* 1.3 68.9 + - + +
116A ALA* 3.2 3.8 + - - +
117A MET* 3.2 46.0 + - + +
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU 2.9 20.0 + - - +
111A ALA* 4.0 2.0 - - - +
113A PHE* 1.3 78.2 - - + +
115A GLY* 1.3 63.2 + - - +
117A MET* 3.0 17.2 + - - +
118A VAL* 3.1 19.9 + - + +
126A LEU* 3.8 23.3 - - + -
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA 2.8 20.3 + - - -
114A ALA* 1.3 74.5 - - - +
116A ALA* 1.3 61.8 + - - +
118A VAL 3.2 8.1 + - - +
123A ARG* 3.2 28.9 - - - +
126A LEU* 3.6 21.2 - - - +
178A TRP* 3.6 14.8 - - - -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 5.4 3.3 - - - -
68A VAL* 3.7 25.1 - - + +
73A TYR* 3.6 35.2 - - + +
112A GLY 3.0 20.0 + - - +
113A PHE 3.2 5.1 + - - +
115A GLY* 1.3 76.8 - - - +
117A MET* 1.3 62.0 + - + +
118A VAL 3.4 1.7 + - - +
178A TRP* 3.7 10.0 - - - +
183A PRO* 4.4 11.6 - - + +
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Residues in contact with MET 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.9 31.9 - - + -
63A VAL* 6.1 0.7 - - - +
68A VAL* 3.8 23.8 - - - -
70A ALA* 5.0 10.3 - - + -
73A TYR* 5.7 1.1 - - - -
113A PHE* 3.2 36.8 - - + +
114A ALA* 3.0 11.2 + - - +
116A ALA* 1.3 78.1 - - - +
118A VAL* 1.3 61.1 + - + +
119A PRO* 3.6 9.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il