Contacts of the helix formed by residues 98 - 116 (chain A) in PDB entry 3Q0U
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR* 1.3 78.5 + - - +
99A ARG* 1.3 59.2 + - + +
100A GLU* 3.1 13.4 + - - +
101A ASN* 2.8 40.4 + - - +
102A MET 2.9 23.6 + - - -
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Residues in contact with ARG 99 (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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97A THR 4.0 0.4 + - - -
98A ASP* 1.3 73.6 - - + +
100A GLU* 1.3 69.3 + - + +
102A MET* 3.3 9.7 + - - +
103A TRP* 3.1 30.2 + - - -
156A GLU* 4.2 6.1 - - - +
159A ARG* 5.7 2.5 - - - +
161A ALA* 4.0 11.1 + - - +
208A VAL* 4.6 9.8 - - + +
212A TYR* 3.5 72.3 + - + +
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Residues in contact with GLU 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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98A ASP* 3.1 9.2 + - - +
99A ARG* 1.3 83.1 - - + +
101A ASN* 1.3 58.8 + - - +
103A TRP* 3.4 2.3 + - - +
104A ARG* 2.9 62.0 + - - +
204A VAL* 3.7 15.4 - - + +
205A HIS* 6.4 0.7 - - - -
208A VAL* 3.8 26.4 - - + +
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Residues in contact with ASN 101 (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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97A THR* 2.9 26.5 + - - +
98A ASP* 2.8 27.0 + - - +
100A GLU* 1.3 72.0 - - - +
102A MET* 1.3 57.5 + - - +
104A ARG* 3.7 20.6 + - - +
105A THR* 2.9 45.1 + - - -
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Residues in contact with MET 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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97A THR* 3.7 23.3 - - + +
98A ASP 2.9 8.6 + - - +
99A ARG* 3.3 9.8 + - - +
101A ASN* 1.3 79.0 - - - +
103A TRP* 1.3 97.5 + - + +
105A THR* 3.3 2.9 + - - -
106A GLY 3.2 15.6 + - - -
152A VAL* 3.9 21.1 - - + -
156A GLU* 4.1 13.2 - - - +
212A TYR* 3.9 10.1 - - - +
217A LL3 3.4 38.4 - - + +
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Residues in contact with TRP 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 ARG 3.1 22.2 + - - -
100A GLU 3.9 4.7 - - - +
102A MET* 1.3 82.3 - - + +
104A ARG* 1.3 67.2 + - - +
106A GLY* 3.2 2.0 + - - +
107A ILE* 2.9 36.9 + - + +
149A THR* 4.0 12.1 - - + -
152A VAL* 3.6 34.3 - - + -
153A ILE* 4.1 13.7 - - + -
156A GLU* 4.9 1.1 - - + -
204A VAL* 5.3 1.1 - - + -
207A TRP* 3.6 36.8 - + + -
208A VAL* 4.4 15.0 - - + -
211A ILE* 3.8 20.1 - - + +
212A TYR* 2.9 38.5 + + - -
217A LL3 3.7 33.4 - + + -
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Residues in contact with ARG 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 GLU* 2.9 61.5 + - - +
101A ASN* 3.7 19.1 + - - +
103A TRP* 1.3 77.3 - - - +
105A THR* 1.3 57.5 + - - +
107A ILE* 3.4 1.4 + - - +
108A ASN* 2.8 31.8 + - + +
200A LEU* 4.2 19.3 - - + +
201A ASP* 3.3 29.4 + - - +
204A VAL* 3.7 38.4 - - + +
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Residues in contact with THR 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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90A LEU* 3.5 31.2 - - + -
101A ASN* 2.9 31.4 + - - -
102A MET* 3.8 4.9 - - - -
104A ARG* 1.3 76.8 - - - +
106A GLY* 1.3 61.6 + - - +
108A ASN* 3.4 8.9 + - + +
109A VAL* 3.2 23.5 + - + +
217A LL3 5.3 0.9 - - - -
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Residues in contact with GLY 106 (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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87A LEU* 4.7 2.0 - - - -
90A LEU* 3.6 15.6 - - - +
102A MET 3.2 6.9 + - - -
103A TRP 3.2 6.0 + - - -
105A THR* 1.3 73.9 - - - +
107A ILE* 1.3 65.3 + - - +
109A VAL* 3.2 19.6 + - - +
110A PHE* 3.4 11.1 - - - -
217A LL3 3.6 28.4 - - - +
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Residues in contact with ILE 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 TRP* 2.9 21.5 + - + +
104A ARG 4.0 0.7 - - - +
106A GLY* 1.3 74.5 - - - +
108A ASN* 1.3 63.6 + - - +
110A PHE* 3.0 6.9 + - - +
111A PHE* 3.0 19.7 + - + +
179A ASN* 4.0 15.3 - - - +
183A LEU* 5.1 5.2 - - + -
200A LEU* 3.7 20.9 - - + -
203A LEU* 4.2 17.7 - - + -
204A VAL* 3.9 24.9 - - + +
207A TRP* 3.9 37.9 - - + +
217A LL3 3.7 25.3 - - + +
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Residues in contact with ASN 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 ARG* 2.8 20.9 + - + +
105A THR* 3.4 11.4 - - - +
106A GLY 3.2 0.2 - - - -
107A ILE* 1.3 74.1 - - - +
109A VAL* 1.3 65.3 + - - +
111A PHE* 3.6 27.6 - - - -
112A GLU* 2.8 41.6 + - - +
200A LEU* 3.7 19.2 - - + +
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Residues in contact with VAL 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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83A ALA* 3.5 16.2 - - - +
86A ALA* 3.5 36.3 - - + +
87A LEU* 3.8 8.1 - - + +
90A LEU* 3.7 25.6 - - + -
105A THR* 3.2 16.4 + - + +
106A GLY 3.2 9.6 + - - +
108A ASN* 1.3 75.3 - - - +
110A PHE* 1.3 66.9 + - + +
112A GLU* 4.1 2.3 - - - +
113A THR* 2.7 38.8 + - - +
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Residues in contact with PHE 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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83A ALA* 3.7 17.3 - - + -
87A LEU* 4.0 24.5 - - + -
106A GLY 3.4 17.7 - - - -
107A ILE 3.0 6.1 + - - +
109A VAL* 1.3 81.0 - - + +
111A PHE* 1.3 65.4 + - - +
113A THR* 4.7 1.6 - - - -
114A PHE* 3.0 45.2 + + + +
145A TRP* 3.5 46.0 - + - -
183A LEU* 4.5 4.5 - - + -
187A PHE* 4.8 0.7 - - - -
217A LL3 3.4 68.2 - + + +
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Residues in contact with PHE 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 ILE* 3.0 12.8 + - + +
108A ASN* 3.6 29.6 - - - +
110A PHE* 1.3 75.2 - - - +
112A GLU* 1.3 72.8 + - - +
115A GLY* 2.9 28.8 + - - -
183A LEU* 3.9 26.3 - - + +
187A PHE* 3.4 17.0 - + - -
196A GLU* 3.7 33.9 - - + -
197A ALA* 5.7 0.9 - - - -
199A VAL* 3.5 23.6 - - + -
200A LEU* 4.2 24.2 - - + -
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ASN* 2.8 43.7 + - - +
109A VAL* 4.2 2.5 - - - +
111A PHE* 1.3 91.6 - - - +
113A THR* 1.3 63.2 + - - +
115A GLY* 5.0 0.4 - - - -
116A SER* 2.7 39.9 + - - +
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Residues in contact with THR 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A VAL* 3.7 17.3 - - + +
82A GLN* 3.8 26.2 + - - +
83A ALA* 3.7 39.6 - - + +
86A ALA* 4.7 5.5 - - - +
109A VAL* 2.7 27.4 + - - +
110A PHE 4.4 0.2 - - - -
112A GLU* 1.3 79.5 - - - +
114A PHE* 1.3 62.2 + - - +
116A SER* 3.4 2.4 + - - -
117A HIS* 3.2 27.6 - - + +
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Residues in contact with PHE 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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76A LEU* 5.7 1.8 - - + -
79A VAL* 3.4 38.8 - - + -
80A VAL* 4.2 9.2 - - + -
83A ALA* 4.0 9.4 - - + -
110A PHE* 3.0 31.5 + + + +
113A THR* 1.3 75.9 - - + +
115A GLY* 1.3 57.9 + - - +
117A HIS 3.0 28.5 + - - +
118A LYS* 3.3 3.5 + - - +
121A THR* 3.2 17.7 + - + +
138A TRP* 4.0 17.7 - + - -
145A TRP* 3.8 22.7 - + - -
183A LEU* 5.4 0.9 - - + -
184A PHE* 3.7 20.6 - + + -
187A PHE* 3.8 14.7 - - + -
217A LL3 3.7 25.4 - + - -
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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 PHE 2.9 21.4 + - - -
112A GLU* 3.8 1.1 - - - -
114A PHE* 1.3 76.8 - - - +
116A SER* 1.3 56.7 + - - +
117A HIS 3.3 0.7 - - - -
118A LYS* 3.0 32.4 + - - +
187A PHE* 3.5 22.1 - - - -
196A GLU* 5.0 0.9 - - - -
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Residues in contact with SER 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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34A GLU* 4.8 0.5 - - - +
82A GLN* 6.1 0.9 - - - -
112A GLU* 2.7 30.8 + - - -
113A THR* 3.8 5.8 - - - -
114A PHE 3.1 0.4 - - - -
115A GLY* 1.3 76.2 - - - +
117A HIS* 1.3 77.8 + - - +
118A LYS 3.8 0.9 - - - -
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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