Contacts of the helix formed by residues 92 - 112 (chain A) in PDB entry 4PYP
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 ARG 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.2 43.9 + - + +
88A ASN* 4.4 2.8 + - - +
91A GLY* 1.3 71.6 - - - -
93A ARG* 1.3 66.1 + - - +
95A SER* 3.0 7.2 + - - -
96A MET* 3.0 28.6 + - + +
139A PHE* 4.7 6.8 - - - +
142A MET* 3.4 16.6 - - - +
143A TYR* 3.5 30.7 - - + +
146A GLU* 2.8 28.4 + - - +
210A SER* 3.8 22.2 - - - +
212A ARG* 4.9 2.2 + - - +
213A PHE* 3.1 39.4 - - - +
217A ASN* 4.0 19.6 + - - +
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 1.3 73.8 - - - +
94A ASN* 1.3 100.5 + - - +
95A SER 2.9 10.7 + - - -
96A MET* 3.2 9.9 + - - +
97A LEU* 2.9 39.1 + - - +
143A TYR* 3.5 26.3 - - + +
204A LEU* 3.7 27.8 + - + +
205A PRO* 5.0 9.4 + - - +
207A CYS* 2.9 30.0 + - - -
208A PRO 4.3 0.2 - - - +
209A GLU* 3.4 39.2 + - + +
210A SER 5.5 1.2 - - - +
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Residues in contact with ASN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.1 26.0 + - + +
91A GLY* 5.0 1.6 - - - -
92A ARG 3.4 0.4 - - - -
93A ARG* 1.3 104.7 + - - +
95A SER* 1.3 57.8 + - - +
97A LEU* 4.3 5.9 - - - +
98A MET* 3.4 35.5 + - + +
209A GLU* 3.3 30.6 + - - +
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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
----------------------------------------------------------
86A PHE* 3.6 20.2 + - - +
90A PHE* 3.7 7.3 - - - +
91A GLY 2.6 22.2 + - - -
92A ARG 3.0 8.3 + - - -
93A ARG 2.9 0.4 - - - -
94A ASN* 1.3 77.2 - - - +
96A MET* 1.3 66.4 + - - +
97A LEU 3.1 1.1 - - - -
98A MET* 3.2 6.9 + - - +
99A MET* 2.8 30.4 + - - +
139A PHE* 3.7 31.0 - - - -
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Residues in contact with MET 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.4 48.5 - - + +
22A GLY* 5.4 1.8 - - - -
92A ARG 3.0 16.9 + - - +
93A ARG* 3.7 4.7 - - - +
95A SER* 1.3 75.2 - - - +
97A LEU* 1.3 62.3 + - - +
99A MET* 3.4 7.9 + - - +
100A ASN* 3.0 18.4 + - - +
132A TYR* 5.0 1.7 - - - -
136A THR* 5.8 2.5 - - - +
139A PHE* 4.0 24.4 - - + -
140A VAL* 3.7 22.2 - - + +
143A TYR* 4.4 24.2 - - - -
200A GLN* 3.6 15.5 + - - +
204A LEU* 3.7 19.5 - - + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 2.9 34.9 + - - +
94A ASN* 4.3 4.9 - - - +
96A MET* 1.3 78.0 - - - +
98A MET* 1.3 63.1 + - - +
99A MET 3.2 0.7 + - - -
100A ASN* 3.2 22.0 + - - +
101A LEU 4.6 0.2 + - - -
201A CYS* 4.0 38.0 - - - +
204A LEU* 3.3 23.5 - - + +
205A PRO* 3.7 26.9 - - + -
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Residues in contact with MET 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 5.2 5.6 - - - -
90A PHE* 3.7 40.6 - - + -
94A ASN* 3.4 23.2 + - + +
95A SER* 3.2 10.2 + - - +
97A LEU* 1.3 79.9 - - - +
99A MET* 1.3 84.5 + - + +
100A ASN 3.1 1.3 - - - -
101A LEU* 3.2 24.9 + - - +
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Residues in contact with MET 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 4.5 18.2 - - + -
95A SER* 2.8 20.1 + - - +
96A MET* 3.4 4.5 + - - +
97A LEU 3.1 0.2 - - - -
98A MET* 1.3 106.2 - - + +
100A ASN* 1.3 56.4 + - - +
101A LEU* 3.0 7.6 - - + -
102A LEU* 2.8 45.9 + - + +
132A TYR* 3.1 27.9 - - + -
135A LEU* 4.1 20.2 - - + -
136A THR* 5.8 1.1 - - - +
139A PHE* 3.7 25.6 - - + -
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Residues in contact with ASN 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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25A GLN* 4.5 0.2 - - - +
96A MET 3.0 19.0 + - - +
97A LEU* 3.2 15.8 + - - +
98A MET 3.1 0.2 - - - -
99A MET* 1.3 75.2 - - - +
101A LEU* 1.3 59.1 + - - +
103A ALA* 3.1 6.0 + - - +
104A PHE* 2.9 40.3 + - + -
132A TYR* 4.1 9.6 + - - -
197A ALA* 3.6 36.6 + - - +
200A GLN* 3.0 34.1 + - - +
201A CYS* 3.8 20.3 - - - -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU 4.6 0.2 + - - -
98A MET 3.2 17.4 + - - +
99A MET* 3.0 3.3 - - + -
100A ASN* 1.3 78.4 - - - +
102A LEU* 1.3 79.4 + - + +
104A PHE* 3.4 5.0 + - + +
105A VAL* 3.0 45.6 + - + +
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Residues in contact with LEU 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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99A MET* 2.8 42.2 + - + +
101A LEU* 1.3 91.1 - - + +
103A ALA* 1.3 64.6 + - - +
105A VAL* 3.2 2.6 + - + +
106A SER* 3.1 26.8 + - - -
128A ILE* 3.8 21.3 - - + +
131A VAL* 3.6 33.9 - - + -
132A TYR* 3.7 23.1 - - + +
135A LEU* 4.3 0.9 - - + -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 5.1 1.6 - - - +
99A MET 3.5 2.4 + - - -
100A ASN* 3.1 10.9 + - - +
102A LEU* 1.3 78.7 - - - +
104A PHE* 1.3 62.2 + - - +
106A SER* 3.1 7.7 + - - -
107A ALA* 3.0 24.7 + - - +
129A ILE* 4.2 10.5 - - + -
132A TYR* 3.9 23.6 - - + -
193A ILE* 4.1 13.0 - - + +
197A ALA* 4.1 22.9 - - + -
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Residues in contact with PHE 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 ASN* 2.9 40.2 + - + +
101A LEU* 4.0 5.6 - - - +
102A LEU 3.2 0.2 - - - -
103A ALA* 1.3 78.4 - - - +
105A VAL* 1.3 65.2 + - + +
107A ALA* 3.2 5.5 + - + +
108A VAL* 3.1 34.3 + - + +
194A PHE* 4.2 22.9 - + + -
197A ALA* 3.6 22.9 - - + -
198A LEU* 3.5 42.8 - - + -
201A CYS* 4.4 9.2 - - + -
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Residues in contact with VAL 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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101A LEU* 3.0 39.4 + - + +
102A LEU* 3.2 4.7 + - + +
104A PHE* 1.3 77.1 - - + +
106A SER* 1.3 59.4 + - - +
108A VAL* 4.1 6.3 - - + +
109A LEU* 3.3 36.0 + - + +
128A ILE* 4.9 13.0 - - + -
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Residues in contact with SER 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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102A LEU 3.1 12.1 + - - -
103A ALA 3.1 9.7 + - - -
105A VAL* 1.3 77.8 - - - +
107A ALA* 1.3 66.3 + - - +
108A VAL 3.1 1.6 - - - -
109A LEU* 3.1 0.7 + - - +
110A MET* 2.9 33.4 + - - +
125A GLY* 3.2 34.3 - - - -
128A ILE* 4.1 5.3 - - - +
129A ILE* 3.3 30.6 - - - +
193A ILE* 5.5 0.9 - - - +
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Residues in contact with ALA 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 ALA 3.0 14.5 + - - +
104A PHE* 3.6 7.9 - - + +
106A SER* 1.3 81.7 + - - +
108A VAL* 1.3 59.8 + - + +
110A MET* 4.2 6.9 - - - +
111A GLY* 3.0 11.3 + - - -
190A LEU 4.9 0.2 - - - -
191A SER* 2.6 51.7 + - - +
193A ILE* 4.3 11.2 - - + -
194A PHE* 4.6 9.6 - - + +
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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 PHE* 3.1 23.4 + - + +
105A VAL* 4.2 6.5 - - + +
107A ALA* 1.3 77.1 - - + +
109A LEU* 1.3 66.5 + - + +
112A PHE* 3.1 50.1 + - + +
121A MET* 4.6 0.5 - - - +
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Residues in contact with LEU 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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105A VAL* 3.3 25.2 + - + +
106A SER 3.1 5.4 + - - +
108A VAL* 1.3 80.6 - - + +
110A MET* 1.3 60.0 + - - +
113A SER* 3.6 2.1 - - - -
121A MET* 3.2 72.3 - - + +
124A LEU* 3.6 35.7 - - + -
125A GLY* 4.1 8.7 - - - +
128A ILE* 4.3 12.3 - - + -
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Residues in contact with MET 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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29A ASN* 5.2 1.6 - - - +
106A SER* 2.9 25.7 + - - +
107A ALA* 4.3 3.4 - - - +
109A LEU* 1.3 75.4 - - - +
111A GLY* 1.3 58.3 + - - +
112A PHE 3.1 3.8 - - - -
113A SER* 2.0 34.4 + - - -
114A LYS 4.3 0.3 + - - -
121A MET 4.3 0.2 - - - -
122A LEU* 4.0 26.5 - - + +
125A GLY* 4.0 14.1 - - - +
126A ARG* 3.9 31.0 - - - +
129A ILE* 4.7 11.7 - - + -
186A TRP* 4.5 1.2 - - - -
187A PRO* 4.5 3.6 - - - +
190A LEU* 3.1 53.2 - - + +
193A ILE* 4.8 7.4 - - + -
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Residues in contact with GLY 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 ALA 3.0 11.8 + - - -
108A VAL 3.9 0.7 - - - -
110A MET* 1.3 75.4 - - - +
112A PHE* 1.3 69.2 + - - +
113A SER 3.5 0.4 - - - -
114A LYS* 3.4 16.1 - - - +
187A PRO* 3.5 25.8 - - - +
188A LEU* 5.3 4.2 - - - +
191A SER* 2.9 22.6 + - - -
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Residues in contact with PHE 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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108A VAL* 3.1 40.8 + - + +
111A GLY* 1.3 83.5 - - - +
113A SER* 1.3 56.6 + - - +
114A LYS* 3.0 25.8 - - + -
115A LEU* 5.8 2.9 - - + -
116A GLY* 3.1 18.9 + - - -
121A MET* 3.1 18.7 - - + +
191A SER* 5.9 0.7 - - - -
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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
------------------------------------------------------------
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