Contacts of the helix formed by residues 91 - 111 (chain A) in PDB entry 3PJA
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 TRP 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.1 17.5 - - + -
28A VAL* 3.7 16.4 - - + -
31A LEU* 6.1 2.2 - - + -
75A LEU* 3.9 16.2 - - + -
79A PHE* 3.6 36.1 - + - -
84A TYR* 3.3 63.8 + + - -
87A PHE* 3.6 26.9 - - + -
88A HIS* 3.0 20.0 + - - -
90A HIS* 1.3 77.1 - - - +
92A ARG* 1.3 71.6 + - - +
93A PHE 3.3 2.2 - - - -
94A VAL* 3.1 10.7 + - + -
95A LEU* 2.8 42.4 + - + +
133A PHE* 3.4 16.6 - + - -
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Residues in contact with ARG 92 (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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88A HIS* 2.9 47.5 + - + +
89A GLU* 3.5 34.6 + - - +
90A HIS 3.6 1.2 - - - -
91A TRP* 1.3 80.5 - - - +
93A PHE* 1.3 66.1 + - - +
95A LEU* 3.1 3.6 + - - +
96A GLN* 2.9 46.0 + - - +
136A ASP* 4.2 6.5 + - - -
138A GLU* 4.4 8.5 - - - +
139A ASP* 3.0 21.8 + - - +
142A SER* 4.9 2.0 + - - -
188A ASN* 3.3 27.7 - - - +
190A SER* 3.9 11.3 + - - -
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Residues in contact with PHE 93 (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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32A GLU* 3.8 28.3 - - + +
89A GLU 5.0 1.6 + - - -
90A HIS 6.1 0.2 - - - +
91A TRP 3.3 0.6 - - - -
92A ARG* 1.3 80.4 - - - +
94A VAL* 1.3 73.8 + - + +
96A GLN* 3.1 10.1 + - + +
97A ARG* 3.0 67.3 + - + +
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Residues in contact with VAL 94 (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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28A VAL* 3.4 20.6 - - + -
31A LEU* 3.9 25.4 - - + +
32A GLU* 3.4 57.4 - - + +
35A ALA* 4.7 4.3 - - + -
90A HIS 4.6 1.1 - - - +
91A TRP* 3.1 13.2 + - + +
93A PHE* 1.3 79.5 - - + +
95A LEU* 1.3 65.8 + - - +
97A ARG* 3.1 5.9 + - - +
98A LEU* 2.8 33.4 + - + +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 5.8 7.0 - - + -
84A TYR* 3.8 19.3 - - - +
88A HIS* 4.9 0.2 - - + -
91A TRP* 2.8 34.3 + - + +
92A ARG 3.4 4.0 - - - +
94A VAL* 1.3 73.3 - - - +
96A GLN* 1.3 62.4 + - - +
98A LEU* 3.1 13.3 + - + +
99A VAL* 2.9 25.1 + - - +
123A LEU* 4.5 16.4 - - + -
125A ILE* 4.9 6.1 - - + -
133A PHE* 4.8 13.5 - - + -
134A HIS 4.6 2.0 - - - +
135A LEU* 3.8 29.4 - - + -
139A ASP* 3.3 26.9 - - + +
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Residues in contact with GLN 96 (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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92A ARG* 2.9 43.9 + - - +
93A PHE* 3.5 9.6 - - + +
95A LEU* 1.3 74.8 - - - +
97A ARG* 1.3 63.6 + - - +
99A VAL* 3.1 6.4 + - - +
100A PHE* 2.9 18.8 + - - +
139A ASP* 3.2 43.8 + - + +
142A SER* 3.3 31.9 + - - -
143A GLY* 3.6 8.3 - - - +
146A ILE* 4.6 6.9 - - + +
194A ARG* 3.6 18.4 + - - +
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Residues in contact with ARG 97 (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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32A GLU 4.9 0.6 + - - -
35A ALA* 4.7 14.4 + - + +
36A ARG* 3.6 35.6 - - - +
39A LEU* 3.8 31.4 - - - +
93A PHE* 3.0 55.4 + - + +
94A VAL* 3.6 9.9 - - - +
96A GLN* 1.3 75.3 - - - +
98A LEU* 1.3 57.8 + - - +
100A PHE* 3.0 20.9 + - - +
101A LEU* 2.8 35.5 + - + +
146A ILE* 4.9 10.5 - - + -
182B ARG* 5.9 0.4 - - - +
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Residues in contact with LEU 98 (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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31A LEU* 4.1 28.9 - - + +
35A ALA* 3.9 24.7 - - + -
38A ILE* 5.0 1.1 - - + -
65A PHE* 4.3 18.7 - - + -
68A VAL* 4.2 25.4 - - + -
72A LEU* 5.2 5.6 - - + -
94A VAL* 2.8 25.4 + - + +
95A LEU* 3.4 12.8 - - + +
97A ARG* 1.3 72.9 - - - +
99A VAL* 1.3 67.8 + - - +
101A LEU* 3.1 10.6 + - + +
102A ALA* 2.8 23.9 + - - +
123A LEU* 4.0 19.3 - - + -
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Residues in contact with VAL 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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95A LEU 2.9 19.7 + - - +
96A GLN 3.3 7.2 - - - +
98A LEU* 1.3 75.1 - - - +
100A PHE* 1.3 66.5 + - - +
102A ALA* 3.1 1.9 + - - +
103A ALA* 2.9 25.0 + - + +
119A VAL* 4.1 16.7 - - + +
123A LEU* 4.7 3.5 - - + +
135A LEU* 3.8 35.9 - - + -
139A ASP 4.2 9.0 - - - +
140A TYR* 3.7 38.8 - - + +
143A GLY* 3.8 10.1 - - - -
144A VAL* 4.4 2.2 - - + +
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Residues in contact with PHE 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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39A LEU* 4.0 14.8 - - + -
96A GLN 2.9 11.9 + - - +
97A ARG* 3.0 21.1 - - - +
99A VAL* 1.3 77.7 - - - +
101A LEU* 1.3 95.7 + - + +
103A ALA* 3.0 4.2 + - - +
104A PHE* 2.8 34.1 + + + +
143A GLY* 3.6 15.9 - - - +
146A ILE* 3.5 23.1 - - + -
147A LEU* 3.4 33.0 - - + -
150A GLU* 3.5 45.3 - - + -
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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
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35A ALA* 3.3 38.4 - - + +
38A ILE* 3.6 21.3 - - + -
39A LEU* 3.8 27.4 - - + +
42A LEU* 3.7 8.9 - - + +
65A PHE* 3.9 12.6 - - + -
97A ARG* 2.8 25.6 + - + +
98A LEU* 3.6 13.2 - - + +
100A PHE* 1.3 97.6 - - + +
102A ALA* 1.3 64.5 + - - +
104A PHE* 3.0 6.3 + - + +
105A VAL* 2.9 25.6 + - - +
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Residues in contact with ALA 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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65A PHE* 3.6 22.3 - - + -
98A LEU 2.8 15.6 + - - +
99A VAL 3.5 6.7 - - - +
101A LEU* 1.3 71.0 - - - +
103A ALA* 1.3 65.0 + - - +
105A VAL* 3.1 7.9 + - - +
106A VAL* 3.0 25.7 + - - +
114A VAL* 4.7 0.7 - - - -
119A VAL* 4.2 19.7 - - + -
122A ILE* 4.1 23.9 - - + +
123A LEU* 4.7 1.8 - - + -
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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
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99A VAL* 2.9 17.3 + - + +
100A PHE* 3.4 10.1 - - - +
102A ALA* 1.3 75.0 - - - +
104A PHE* 1.3 57.7 + - - +
106A VAL* 3.1 4.0 + - - +
107A TYR* 2.8 30.0 + - - +
112A THR 4.9 1.0 - - - +
113A LEU* 5.0 4.3 - - + -
114A VAL* 3.4 28.7 + - + +
140A TYR* 6.4 0.2 - - + -
143A GLY 5.3 1.1 - - - +
144A VAL* 5.6 4.3 - - + -
147A LEU* 3.9 24.6 - - + +
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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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39A LEU* 5.7 0.7 - - + -
42A LEU* 3.5 40.8 - - + -
43A GLN* 4.8 3.6 - - - -
45A VAL* 4.0 22.7 - - + -
46A HIS* 4.6 2.7 - - - -
100A PHE* 2.8 30.1 + + + +
101A LEU* 3.2 11.7 - - + +
103A ALA* 1.3 76.0 - - - +
105A VAL* 1.3 61.8 + - - +
107A TYR* 3.1 3.4 + - + +
108A LEU* 2.9 42.2 + - + +
147A LEU* 3.6 21.9 - - + +
150A GLU* 4.1 25.4 - - + -
151A LEU* 4.0 19.5 - - + -
154A LEU* 4.4 3.8 - - + -
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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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42A LEU* 3.5 27.4 - - + -
58A CYS* 4.3 8.5 - - + +
61A ALA* 3.7 21.8 - - + -
62A ARG* 4.0 21.8 - - + +
65A PHE* 4.4 11.0 - - + -
101A LEU 2.9 10.5 + - - +
102A ALA* 3.3 9.0 - - - +
104A PHE* 1.3 76.2 - - - +
106A VAL* 1.3 64.6 + - - +
108A LEU* 3.1 9.0 + - - +
109A GLU* 3.0 51.3 + - + +
122A ILE* 6.2 1.3 - - + -
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Residues in contact with VAL 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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62A ARG* 4.2 20.6 - - - +
102A ALA 3.0 13.8 + - - +
103A ALA 3.1 7.4 + - - +
105A VAL* 1.3 75.5 - - + +
107A TYR* 1.3 58.8 + - - +
109A GLU* 3.1 8.8 + - - +
110A THR* 2.7 47.1 + - + +
112A THR* 3.6 17.9 - - - +
114A VAL* 3.7 40.6 - - + +
122A ILE* 4.3 6.5 - - + -
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Residues in contact with TYR 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 2.8 13.3 + - - +
104A PHE* 3.1 10.7 + - - +
106A VAL* 1.3 76.9 - - - +
108A LEU* 1.3 70.0 + - + +
111A GLU* 2.6 64.2 + - + +
112A THR 3.8 7.9 - - - +
147A LEU* 4.8 4.0 - - + -
151A LEU* 4.0 30.5 - - + -
154A LEU* 5.2 2.5 - - + -
166A ARG* 4.8 6.3 - - - -
169A HIS* 3.7 12.6 + - - +
170A ILE* 3.4 41.2 + - + +
173A PHE* 3.5 47.8 - + - -
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Residues in contact with LEU 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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42A LEU* 4.5 16.8 - - + -
45A VAL* 4.4 13.0 - - + -
54A ILE* 3.9 34.4 - - + +
57A ARG* 6.0 2.0 - - + -
58A CYS* 3.4 28.2 - - - -
104A PHE* 2.9 48.6 + - + +
105A VAL 3.1 2.2 + - - +
107A TYR* 1.3 77.1 - - + +
109A GLU* 1.3 60.4 + - - +
111A GLU* 5.7 0.4 - - - +
154A LEU* 4.0 19.3 - - + -
166A ARG* 4.1 20.0 + - - +
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Residues in contact with GLU 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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55A PRO* 6.3 0.2 - - + -
58A CYS* 3.8 25.6 - - + +
59A LEU* 4.8 7.3 - - - +
62A ARG* 3.1 46.0 + - - -
105A VAL* 3.0 23.6 + - - +
106A VAL* 3.6 7.9 - - - +
107A TYR 2.9 0.8 - - - -
108A LEU* 1.3 81.2 - - - +
110A THR* 1.3 70.7 + - + +
111A GLU* 3.9 1.1 - - - -
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Residues in contact with THR 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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106A VAL* 2.7 25.2 + - + +
109A GLU* 1.3 92.1 - - + +
111A GLU* 1.3 74.0 + - - +
112A THR* 2.7 37.1 + - - +
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Residues in contact with GLU 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 TYR* 2.6 57.9 + - + +
109A GLU 5.6 0.7 - - - -
110A THR* 1.3 76.0 + - - +
112A THR* 1.3 61.0 + - - +
166A ARG* 3.9 30.3 + - - +
169A HIS* 3.0 46.7 + - + +
173A PHE* 4.1 7.1 - - - +
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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