Contacts of the helix formed by residues 100 - 118 (chain B) in PDB entry 3N1Q
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 THR 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASP 5.3 1.3 - - - -
77B LEU* 3.8 14.1 - - + +
99B MET* 1.3 79.7 - - - +
101B GLU* 1.3 65.7 + - - +
102B ARG 3.9 1.6 + - - -
103B CYS* 3.1 26.9 + - - +
104B LYS* 3.2 10.6 + - - +
143B GLU 3.4 17.5 - - - +
144B GLY 2.9 21.6 + - - +
145B ARG* 3.6 12.6 - - + +
186B VAL* 4.0 10.2 - - - +
187B LYS 4.9 0.3 + - - -
189B ASP* 4.3 18.8 + - + +
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASP 5.3 4.3 + - - +
78B VAL* 6.0 6.9 - - + +
99B MET 3.9 0.4 + - - -
100B THR* 1.3 72.7 - - - +
102B ARG* 1.3 63.7 + - - +
104B LYS* 3.1 30.8 + - + +
105B GLU* 3.3 22.0 + - + +
189B ASP* 3.5 15.2 + - - +
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 3.3 2.9 - - - +
101B GLU* 1.3 79.2 + - - +
103B CYS* 1.3 65.1 + - - +
105B GLU* 3.5 7.5 + - - +
106B ARG* 3.2 46.4 + - - +
170B GLY 4.7 4.0 + - - -
172B ASP* 3.1 38.1 + - - -
186B VAL* 4.1 7.7 - - + +
187B LYS* 3.7 36.0 - - - +
188B ALA 4.4 2.9 - - - -
189B ASP* 3.2 21.6 + - - +
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Residues in contact with CYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B MET* 3.8 28.7 - - + -
100B THR* 3.1 23.4 + - - +
102B ARG* 1.3 78.0 - - - +
104B LYS* 1.3 63.8 + - - +
106B ARG* 2.9 4.3 + - - +
107B VAL* 2.8 34.4 + - - +
144B GLY 4.0 5.8 - - - +
145B ARG 4.7 10.5 - - - -
147B LEU* 3.8 19.7 - - - -
171B PHE* 4.5 7.9 - - - -
186B VAL* 4.1 14.7 - - + +
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B VAL* 3.1 56.8 - - - +
79B PRO 3.3 15.1 + - - -
80B ASN* 4.1 15.6 - - + +
99B MET* 3.6 26.4 - - + -
100B THR 3.2 6.7 + - - +
101B GLU* 3.1 17.2 + - + +
103B CYS* 1.3 78.3 - - - +
105B GLU* 1.3 67.0 + - + +
106B ARG 3.0 0.7 + - - -
107B VAL* 3.0 1.1 + - - -
108B ASN* 2.8 41.2 + - - +
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLU* 3.5 24.5 - - + +
102B ARG* 3.7 9.6 - - - +
103B CYS 3.4 0.2 - - - -
104B LYS* 1.3 80.8 - - + +
106B ARG* 1.3 80.2 + - - +
108B ASN* 3.7 9.0 + - - +
109B ALA* 3.2 20.8 + - - +
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Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ARG* 3.2 55.2 + - - +
103B CYS 2.9 9.5 + - - +
105B GLU* 1.3 93.3 + - - +
107B VAL* 1.3 66.4 + - - +
109B ALA* 3.0 7.0 + - - +
110B LEU* 3.0 20.4 + - - +
169B ALA* 3.5 18.1 + - - +
170B GLY* 3.1 27.1 - - - -
171B PHE* 3.3 43.9 - - + +
186B VAL* 4.2 8.1 - - + -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASN* 4.7 2.7 - - - +
85B ILE* 3.6 23.1 - - + -
87B PHE* 5.8 0.2 - - + -
99B MET* 3.8 10.1 - - + -
103B CYS* 2.8 27.4 + - - +
104B LYS* 3.7 2.0 - - - +
106B ARG* 1.3 71.1 - - - +
108B ASN* 1.3 54.0 + - - +
110B LEU* 2.9 3.7 + - + +
111B ALA* 2.6 36.9 + - - +
123B LEU* 3.6 17.3 - - + -
125B VAL* 4.8 4.7 - - + -
147B LEU* 3.3 35.4 - - + -
149B ILE* 5.7 0.2 - - + -
171B PHE* 3.6 15.3 - - + -
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Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASN* 3.3 21.8 + - - +
82B ASN* 3.1 32.2 + - - +
85B ILE* 4.1 0.7 - - - +
104B LYS* 2.8 39.3 + - - +
105B GLU* 3.9 8.0 + - - +
107B VAL* 1.3 71.1 - - - +
109B ALA* 1.3 61.1 + - - +
111B ALA* 3.5 2.9 + - - +
112B ILE* 3.3 30.8 + - + +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLU 3.2 10.8 + - - +
106B ARG* 3.0 10.7 + - - +
107B VAL 3.0 0.4 - - - -
108B ASN* 1.3 77.5 - - - +
110B LEU* 1.3 64.6 + - - +
112B ILE* 3.3 12.2 + - - +
113B ALA* 3.0 21.9 + - - +
169B ALA* 4.1 20.4 - - + +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ARG 3.0 8.8 + - - +
107B VAL* 2.9 7.9 + - + +
109B ALA* 1.3 73.2 - - - +
111B ALA* 1.3 60.2 + - - +
113B ALA* 4.1 3.1 - - + -
114B VAL* 2.9 49.4 + - + +
123B LEU* 3.8 18.6 - - + -
149B ILE* 3.5 32.3 - - + -
162B LEU* 4.2 5.6 - - + -
165B LEU* 3.7 36.3 - - + +
166B ALA* 3.8 5.6 - - + +
169B ALA* 3.7 16.3 - - + +
171B PHE* 4.0 19.1 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ASN* 4.1 7.6 - - - +
84B ASP* 4.1 9.4 - - + +
85B ILE* 3.5 32.3 - - + -
107B VAL 2.6 19.6 + - - +
108B ASN 3.5 8.1 - - - +
109B ALA 3.2 0.2 - - - -
110B LEU* 1.3 75.3 - - - +
112B ILE* 1.3 60.8 + - - +
114B VAL* 3.5 3.3 + - - +
115B MET* 3.1 27.7 + - - +
123B LEU* 4.1 14.0 + - + +
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ASN* 6.0 0.2 - - - +
84B ASP* 4.6 13.5 - - - +
108B ASN* 3.3 18.8 + - + +
109B ALA* 3.3 9.4 + - - +
111B ALA* 1.3 74.3 - - - +
113B ALA* 1.3 66.2 + - - +
115B MET* 2.9 11.5 + - - +
116B ASN* 2.9 47.4 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ALA 3.0 16.4 + - - +
110B LEU* 3.2 9.8 + - - +
112B ILE* 1.3 77.9 - - - +
114B VAL* 1.3 60.7 + - - +
116B ASN* 4.1 8.3 - - - +
117B MET* 3.1 22.9 + - - +
165B LEU* 4.0 29.7 - - + +
169B ALA* 5.7 1.6 - - + -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 2.9 35.8 + - + +
111B ALA 3.7 6.1 - - - +
112B ILE 3.1 0.2 - - - -
113B ALA* 1.3 75.2 - - - +
115B MET* 1.3 61.1 + - - +
117B MET* 3.1 6.5 + - - +
118B TRP* 2.9 49.7 + - + +
121B VAL* 4.1 10.3 - - + -
122B ARG* 4.0 7.2 - - - -
123B LEU* 3.8 30.5 - - + +
151B THR* 5.0 2.5 - - + -
162B LEU* 3.7 27.8 - - + -
165B LEU* 4.4 1.6 - - + -
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Residues in contact with MET 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASP* 3.6 31.4 - - - +
111B ALA 3.1 17.0 - - - +
112B ILE* 2.9 8.2 + - - +
114B VAL* 1.3 71.7 - - - +
116B ASN* 1.3 66.7 + - - +
117B MET 2.9 5.5 + - - -
118B TRP 3.3 17.0 - - - +
119B PRO* 3.7 7.7 - - - +
120B GLY* 6.2 2.7 - - - +
121B VAL 3.5 19.5 - - - +
122B ARG* 3.5 34.5 - - + -
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Residues in contact with ASN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 2.9 36.9 + - - +
113B ALA* 4.1 7.8 - - - +
115B MET* 1.3 78.5 - - - +
117B MET* 1.3 59.5 + - - +
119B PRO* 5.3 2.9 - - - +
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Residues in contact with MET 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 5.3 8.7 - - + -
113B ALA 3.1 15.5 + - - +
114B VAL 3.1 10.1 + - - +
115B MET 2.9 1.2 - - - -
116B ASN* 1.3 83.0 - - - +
118B TRP* 1.3 106.2 + - + +
119B PRO* 3.6 7.9 - - - +
161B LEU* 4.4 23.3 - - + -
165B LEU* 4.0 17.7 - - + -
914F GLU* 4.2 8.0 - - - +
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Residues in contact with TRP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 2.9 43.9 + - + +
115B MET 3.3 9.1 - - - +
117B MET* 1.3 104.1 - - + +
119B PRO* 1.3 70.0 - - + +
120B GLY 3.6 0.2 + - - -
121B VAL* 3.1 34.9 + - + +
151B THR* 4.1 12.3 - - + -
158B LYS* 3.4 57.9 - - + +
161B LEU* 3.8 26.9 - - + +
162B LEU* 3.9 10.3 - - + -
165B LEU* 3.7 26.5 - - + -
914F GLU* 6.0 0.4 - - - -
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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