Contacts of the helix formed by residues 104 - 122 (chain B) in PDB entry 3K7G
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 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 5.9 0.2 - - + -
80B GLU* 3.5 28.3 - - + +
81B LEU* 4.1 3.6 - - + -
82B THR* 4.2 0.7 - - - -
103B MET* 1.3 75.9 - - - +
105B GLN* 1.3 65.8 + - - +
106B ARG* 3.8 5.1 + - - +
107B CYS* 3.2 20.4 + - - +
108B LYS* 2.9 21.1 + - - +
147B GLU 4.0 9.0 - - - +
148B GLY 3.0 15.1 + - - +
149B ARG* 3.7 19.6 - - + +
190B VAL* 3.8 10.0 - - - +
191B LYS 5.1 0.5 + - - -
192B SER* 6.2 0.9 - - - -
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU 4.3 3.4 + - - -
82B THR* 4.0 19.9 + - + +
103B MET 3.9 0.4 + - - -
104B THR* 1.3 74.0 - - - +
106B ARG* 1.3 59.0 + - - +
108B LYS* 3.2 25.3 + - - +
109B ASP* 2.8 67.3 + - - +
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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
----------------------------------------------------------
104B THR* 3.3 4.3 + - - +
105B GLN* 1.3 75.7 - - - +
107B CYS* 1.3 66.2 + - - +
109B ASP* 3.2 7.7 + - + +
110B ARG* 3.0 37.1 + - + +
174B GLY 4.4 7.8 + - - -
176B ASP* 2.8 38.8 + - - -
190B VAL* 3.9 12.9 - - + +
191B LYS* 3.5 43.4 - - - +
192B SER 5.7 1.6 - - - -
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Residues in contact with CYS 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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103B MET* 3.9 26.7 - - + -
104B THR* 3.2 22.8 + - - +
106B ARG* 1.3 79.4 - - - +
108B LYS* 1.3 55.2 + - - +
110B ARG* 3.4 1.4 + - - +
111B LEU* 2.9 32.5 + - - +
148B GLY 4.0 6.7 - - - +
149B ARG 4.3 14.4 - - - -
150B ALA 4.5 0.2 - - - -
151B VAL* 4.1 21.8 - - - -
175B PHE* 4.3 14.4 - - - -
190B VAL* 3.7 16.0 - - + +
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 4.1 24.1 + - + -
83B PRO 5.0 5.0 + - - +
84B ASN* 3.7 22.7 - - + +
103B MET* 3.6 19.9 - - + -
104B THR 2.9 12.9 + - - +
105B GLN* 3.4 29.0 + - - +
107B CYS* 1.3 76.8 - - - +
109B ASP* 1.3 58.9 + - - +
111B LEU* 3.4 1.1 + - - +
112B ASN* 2.8 56.5 + - - +
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLN* 2.8 51.9 + - - +
106B ARG* 3.7 7.7 - - + +
108B LYS* 1.3 76.3 - - - +
110B ARG* 1.3 86.9 + - - +
112B ASN* 3.4 7.6 + - - +
113B SER* 3.1 22.9 + - - -
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 3.0 34.4 + - + +
109B ASP* 1.3 98.1 + - - +
111B LEU* 1.3 60.4 + - - +
113B SER* 3.4 21.5 + - - -
114B LEU* 3.0 28.8 + - - +
173B ALA* 2.8 36.1 + - - +
174B GLY* 3.5 24.8 - - - +
175B PHE* 3.6 27.9 - - + -
190B VAL* 4.0 12.3 - - + -
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Residues in contact with LEU 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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84B ASN* 3.9 5.4 - - - +
89B ILE* 3.7 22.2 - - + -
91B PHE* 4.2 2.2 - - + -
103B MET* 3.8 29.4 - - + -
107B CYS* 2.9 19.5 + - - +
108B LYS* 3.7 3.6 - - - +
110B ARG* 1.3 76.8 - - - +
112B ASN* 1.3 60.5 + - - +
114B LEU* 3.3 2.0 + - + -
115B ALA* 2.9 25.1 + - - +
127B LEU* 3.5 23.3 - - + +
129B VAL* 3.9 21.1 - - + -
151B VAL* 3.9 18.8 - - + -
153B ILE* 4.3 5.4 - - + -
175B PHE* 3.6 20.6 - - + -
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Residues in contact with ASN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 3.1 22.1 + - - +
86B ASN* 2.9 30.7 + - - +
89B ILE* 3.6 2.9 - - - +
108B LYS* 2.8 46.9 + - - +
109B ASP* 3.8 7.7 + - - +
111B LEU* 1.3 75.2 - - - +
113B SER* 1.3 65.6 + - - +
115B ALA* 3.3 11.1 + - - +
116B ILE* 3.4 18.8 + - - +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP 3.1 14.7 + - - -
110B ARG* 3.6 25.1 + - - -
112B ASN* 1.3 76.4 - - - +
114B LEU* 1.3 62.3 + - - +
116B ILE* 3.2 21.1 + - - +
117B SER* 3.2 15.6 + - - -
173B ALA* 3.9 16.2 + - - +
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Residues in contact with LEU 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 ARG 3.0 16.7 + - - +
111B LEU* 3.6 6.1 - - + +
113B SER* 1.3 76.7 + - - +
115B ALA* 1.3 58.3 + - - +
117B SER* 3.1 4.7 + - - -
118B VAL* 2.8 45.2 + - + +
127B LEU* 3.9 16.8 - - + -
153B ILE* 3.6 30.7 - - + -
166B LEU* 4.5 2.2 - - + +
169B LEU* 3.6 42.6 - - + +
170B ALA* 3.6 14.4 - - + +
173B ALA* 3.7 10.7 - - + +
175B PHE* 3.9 12.1 - - + -
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASN* 4.2 7.4 - - - +
88B ASP* 4.1 12.9 - - + +
89B ILE* 3.7 28.3 - - + -
111B LEU 2.9 14.2 + - - +
112B ASN 3.5 10.5 - - - +
113B SER 3.2 0.4 - - - -
114B LEU* 1.3 77.5 - - - +
116B ILE* 1.3 61.5 + - + +
118B VAL* 3.5 2.3 + - - +
119B MET* 3.3 30.0 + - + +
127B LEU* 3.8 14.0 + - + +
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP* 5.9 0.4 - - - +
112B ASN 3.4 13.4 + - - +
113B SER* 3.2 12.5 + - - +
114B LEU 3.2 0.8 - - - -
115B ALA* 1.3 77.1 - - + +
117B SER* 1.3 61.1 + - - +
119B MET* 3.3 19.5 + - + +
120B ASN* 2.9 43.9 + - - +
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Residues in contact with SER 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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113B SER* 3.2 13.4 + - - -
114B LEU* 3.1 18.0 + - - -
116B ILE* 1.3 80.4 - - - +
118B VAL* 1.3 55.9 - - - +
120B ASN* 3.3 11.1 + - - +
121B GLN* 2.8 30.5 + - - +
169B LEU* 4.1 20.3 - - - +
172B GLU* 6.6 0.2 - - - -
173B ALA* 5.4 3.2 - - - +
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Residues in contact with VAL 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 LEU* 2.8 33.1 + - + +
115B ALA 3.9 4.3 - - - +
116B ILE 3.2 0.2 - - - -
117B SER* 1.3 74.3 - - - +
119B MET* 1.3 64.7 + - - +
121B GLN* 3.7 1.5 - - - +
122B TRP* 3.0 40.5 + - + +
125B VAL* 4.2 5.4 - - + +
126B LYS* 3.6 11.4 - - - +
127B LEU* 3.6 32.3 - - + +
155B THR* 4.6 3.8 - - + -
166B LEU* 3.6 27.8 - - + -
169B LEU* 4.4 9.4 - - + -
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Residues in contact with MET 119 (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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88B ASP* 3.5 45.5 - - + +
115B ALA 3.3 19.5 + - - +
116B ILE* 3.7 22.0 - - + +
118B VAL* 1.3 76.4 - - - +
120B ASN* 1.3 64.0 + - - +
123B PRO* 3.4 25.5 - - - +
124B GLY 5.6 0.9 - - - +
125B VAL 3.5 21.5 - - - +
126B LYS* 4.3 18.2 - - + -
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Residues in contact with ASN 120 (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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116B ILE* 2.9 33.4 + - - +
117B SER* 3.5 12.8 + - - +
119B MET* 1.3 79.6 - - - +
121B GLN* 1.3 61.5 + - - +
122B TRP 3.5 0.2 + - - -
123B PRO* 3.8 11.2 - - - +
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Residues in contact with GLN 121 (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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44B LEU* 4.3 8.5 - - - +
117B SER 2.8 21.1 + - - +
118B VAL 3.2 4.0 + - - +
120B ASN* 1.3 74.4 - - - +
122B TRP* 1.3 93.7 + - + +
123B PRO* 3.6 5.2 - - - +
165B LEU* 3.6 25.0 - - - +
169B LEU* 3.7 30.3 - - + +
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Residues in contact with TRP 122 (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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118B VAL* 3.0 33.2 + - + +
119B MET 3.5 3.7 - - - +
121B GLN* 1.3 101.0 - - + +
123B PRO* 1.3 71.4 - - - +
124B GLY 3.1 0.3 + - - -
125B VAL* 2.9 38.6 + - + +
155B THR* 3.8 17.9 - - + -
162B LYS* 3.3 63.1 - - + +
165B LEU* 3.8 18.6 - - + +
166B LEU* 3.8 19.3 - - + -
169B LEU* 3.8 17.9 - - + -
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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
------------------------------------------------------------
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