Contacts of the helix formed by residues 95 - 108 (chain A) in PDB entry 3I5G
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 ASN 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TRP* 3.7 0.8 - - - -
75A GLY* 4.5 4.9 - - - -
76A GLN* 3.2 35.2 + - - +
93A PHE* 3.5 9.5 + - - +
94A LEU* 1.3 76.5 - - - +
96A GLU* 1.3 69.4 + - - +
97A ALA* 3.5 10.8 + - - +
98A SER* 2.6 42.7 + - - -
99A ILE* 2.9 22.2 + - - +
706A ARG* 3.8 17.5 - - - +
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Residues in contact with GLU 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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43A PHE* 4.0 18.8 - - + -
95A ASN* 1.3 73.2 - - - +
97A ALA* 1.3 52.6 + - - +
99A ILE* 3.1 11.0 + - - +
100A LEU* 2.8 36.6 + - - +
690A LEU* 3.8 25.2 - - + +
694A ARG* 2.6 41.2 + - - -
699A LEU* 4.1 20.5 - - + +
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Residues in contact with ALA 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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35A TRP* 3.6 33.3 - - + -
43A PHE* 3.7 39.2 - - + +
75A GLY* 5.7 0.9 - - - -
95A ASN* 3.1 10.2 + - - +
96A GLU* 1.3 76.9 - - - +
98A SER* 1.3 53.2 + - - +
100A LEU* 3.0 5.4 + - - +
101A HIS* 2.8 35.2 + - - +
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Residues in contact with SER 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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35A TRP* 2.9 25.1 + - - +
76A GLN 3.5 4.9 + - - -
78A ASN* 3.6 8.2 + - - -
91A LEU* 3.9 9.0 - - - +
93A PHE 3.2 25.3 + - - -
94A LEU 4.7 0.2 - - - -
95A ASN* 2.6 34.9 + - - -
97A ALA* 1.3 73.5 - - - +
99A ILE* 1.3 60.8 + - - +
101A HIS* 3.9 1.6 - - - +
102A ASN* 3.1 25.6 + - - +
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Residues in contact with ILE 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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88A MET* 2.9 54.0 - - + +
91A LEU* 4.4 7.4 - - + -
94A LEU* 4.4 13.5 - - + +
95A ASN 2.9 22.4 + - - +
96A GLU* 3.4 9.9 - - - +
98A SER* 1.3 75.2 - - - +
100A LEU* 1.3 65.2 + - - +
103A LEU* 3.2 15.5 + - + +
690A LEU* 6.1 0.2 - - + -
693A LEU* 3.8 27.4 - - + -
698A VAL* 4.9 2.5 - - + -
699A LEU* 4.3 16.2 - - + -
702A ILE* 3.8 31.9 - - + -
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Residues in contact with LEU 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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41A PHE 3.9 1.1 - - - +
42A GLY* 4.4 0.7 - - - -
43A PHE* 3.8 37.2 - - + +
96A GLU 2.8 12.8 + - - +
97A ALA* 3.0 8.5 + - - +
99A ILE* 1.3 79.5 - - - +
101A HIS* 1.3 58.0 + - - +
103A LEU* 3.8 4.9 - - + +
104A ARG* 2.8 74.7 + - + +
684A ILE* 4.6 7.0 - - + -
686A ALA* 4.2 20.0 - - + -
689A VAL* 4.8 10.8 - - + -
690A LEU* 4.1 19.7 - - + +
693A LEU* 5.6 1.1 - - - -
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Residues in contact with HIS 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 TRP* 3.1 46.5 - + + -
77A ARG* 4.2 9.0 - - - -
83A GLU* 3.0 35.3 + - - -
97A ALA 2.8 14.3 + - - +
98A SER 3.9 3.4 - - - +
99A ILE 3.3 0.2 - - - -
100A LEU* 1.3 72.3 - - - +
102A ASN* 1.3 64.2 + - - +
104A ARG* 2.9 15.9 + - - +
105A SER* 2.6 54.0 + - - -
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Residues in contact with ASN 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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82A PHE 4.7 1.3 + - - -
84A MET* 4.1 4.0 - - - +
85A ASN* 3.1 54.9 + - - +
88A MET* 3.5 30.7 - - + +
91A LEU* 3.6 15.1 - - + +
98A SER 3.1 16.6 + - - +
101A HIS* 1.3 84.6 - - - +
103A LEU* 1.3 62.7 + - - +
105A SER* 3.1 11.4 + - - -
106A ARG* 3.3 18.0 + - - +
114A THR* 5.0 0.9 - - - -
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Residues in contact with LEU 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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88A MET* 3.9 10.5 - - - -
99A ILE* 3.2 23.2 + - + +
100A LEU* 3.8 4.3 - - + +
101A HIS 3.1 0.4 - - - -
102A ASN* 1.3 80.6 - - - +
104A ARG* 1.3 65.7 + - - +
106A ARG* 3.3 5.9 + - - +
107A TYR* 3.1 19.8 + - - +
112A ILE 5.9 0.7 - - - +
114A THR* 3.8 25.1 - - + +
121A ILE* 3.8 37.2 - - + -
123A ILE* 4.2 20.0 - - + +
673A ILE* 5.0 1.8 - - + -
689A VAL* 4.8 9.9 - - + -
693A LEU* 3.9 30.1 - - + -
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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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35A TRP* 6.4 0.6 - - - -
41A PHE* 2.8 37.6 + - - +
43A PHE 3.8 13.1 + - - -
44A VAL* 5.6 1.0 - - - +
62A LYS* 6.2 0.6 - - - +
100A LEU* 2.8 53.4 + - + +
101A HIS* 2.9 14.0 + - - +
103A LEU* 1.3 73.3 - - - +
105A SER* 1.3 56.5 - - - +
107A TYR* 2.7 26.0 + - - +
108A GLU* 2.8 42.4 + - - +
684A ILE* 3.8 33.1 + - + +
686A ALA* 4.0 5.3 - - - +
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Residues in contact with SER 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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83A GLU* 4.4 0.3 + - - -
84A MET* 3.3 29.6 + - - +
101A HIS* 2.6 53.2 + - - -
102A ASN* 3.1 13.0 + - - -
104A ARG* 1.3 76.7 - - - +
106A ARG* 1.3 57.3 + - - +
108A GLU* 3.6 8.6 + - - +
109A SER* 3.3 25.8 + - - -
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Residues in contact with ARG 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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13A LEU* 4.1 16.0 + - - +
14A CYS 5.3 5.7 + - - -
84A MET* 2.9 45.2 + - + +
85A ASN 3.1 23.6 + - - -
86A MET* 3.9 15.7 - - - +
102A ASN* 3.3 19.6 + - - +
103A LEU 3.8 3.6 - - - +
104A ARG 3.0 1.4 - - - -
105A SER* 1.3 79.3 + - - +
107A TYR* 1.3 56.4 + - - +
109A SER* 3.5 4.4 + - - -
111A PHE* 2.7 63.8 + - + +
113A TYR* 3.0 19.3 + - - +
114A THR* 3.0 27.0 + - - +
150A PRO* 4.1 13.5 + - - +
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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 LEU 3.1 11.0 + - - +
104A ARG 2.7 11.0 + - - +
106A ARG* 1.3 69.8 - - - +
108A GLU* 1.3 58.1 + - - +
109A SER 3.1 8.3 + - - -
110A GLY* 3.3 11.2 + - - -
111A PHE 2.9 18.6 + - - +
112A ILE* 4.0 9.9 - - + -
123A ILE* 3.8 23.1 - - + -
124A ASN 2.4 33.8 + - - -
125A PRO* 3.6 21.6 + - + -
126A TYR* 4.6 0.2 - - - -
127A ARG* 5.8 0.2 + - - -
675A PRO* 3.7 11.8 - - + +
680A THR 4.3 0.9 + - - -
681A PRO* 4.1 2.6 - - - +
682A GLY* 3.5 38.7 + - - -
683A LEU 3.7 11.2 - - - -
684A ILE* 3.2 36.6 - - + -
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Residues in contact with GLU 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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62A LYS* 4.3 15.3 + - - -
104A ARG* 2.8 44.7 + - + +
105A SER* 3.6 9.2 + - - +
106A ARG 3.3 0.2 - - - -
107A TYR* 1.3 76.5 - - - +
109A SER* 1.3 59.9 + - - +
110A GLY 3.4 1.6 - - - -
682A GLY* 3.6 23.7 - - - +
683A LEU* 5.9 1.0 - - - +
684A ILE* 4.3 11.0 + - + +
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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