Contacts of the helix formed by residues 59 - 76 (chain B) in PDB entry 4GKH
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 GLY 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS* 1.3 74.4 - - - +
60B SER* 1.3 62.7 + - - -
62B ALA* 3.0 19.6 + - - +
63B ASN* 3.8 6.4 + - - -
89B ARG* 4.7 2.4 + - - -
92B ASP* 3.0 29.6 + - - -
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS 3.3 1.0 + - - -
59B GLY* 1.3 71.9 - - - -
61B VAL* 1.3 67.2 + - - +
63B ASN* 3.0 36.0 + - - +
64B ASP* 3.4 10.5 + - - +
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY* 3.6 18.4 - - - +
38B ALA* 3.5 31.6 - - + +
57B GLY* 3.7 15.9 - - - -
58B LYS 3.0 15.8 + - - +
60B SER* 1.3 80.2 - - - +
62B ALA* 1.3 64.4 + - - +
64B ASP* 3.1 18.6 + - + +
65B VAL* 3.0 22.8 + - + +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLY* 3.5 24.1 - - - +
58B LYS 3.6 2.6 + - - -
59B GLY 3.0 16.3 + - - +
61B VAL* 1.3 78.7 - - - +
63B ASN* 1.3 59.1 + - - +
65B VAL 3.4 0.7 + - - -
66B THR* 2.9 27.7 + - - -
89B ARG* 3.8 20.4 - - - +
92B ASP 4.0 7.4 - - - +
93B ASP 4.0 3.4 - - - -
94B ALA* 3.6 19.3 - - - +
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 2.7 31.6 + - - +
59B GLY 4.3 2.6 + - - -
60B SER* 3.0 23.9 + - - +
62B ALA* 1.3 75.2 - - - +
64B ASP* 1.3 60.6 + - - +
66B THR* 3.2 4.2 + - - -
67B ASP* 2.9 39.2 + - - +
89B ARG* 3.1 19.1 + - - +
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY* 5.8 1.7 - - - -
60B SER* 3.4 8.4 + - - +
61B VAL* 3.1 29.7 + - + +
63B ASN* 1.3 77.1 - - - +
65B VAL* 1.3 64.2 + - + +
67B ASP* 3.2 15.0 + - - +
68B GLU* 3.0 21.5 + - - +
218B GLY* 5.1 1.7 - - - -
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 4.0 19.5 - - + -
55B LYS* 4.4 15.9 - - + +
56B HIS 4.5 0.2 - - - -
57B GLY* 3.8 22.2 - - - +
61B VAL* 3.0 16.9 + - + +
62B ALA 3.8 4.5 - - - +
64B ASP* 1.3 76.6 - - + +
66B THR* 1.3 58.5 + - - +
68B GLU* 3.3 8.5 + - - +
69B MSE 3.0 26.0 + - - +
87B PHE* 4.2 2.2 - - + -
94B ALA* 4.1 16.8 - - + +
96B LEU* 3.6 32.5 - - + +
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MSE 3.8 22.4 - - + -
70A VAL* 3.6 26.5 - - + -
73A ASN* 4.9 7.0 - - - +
62B ALA 2.9 19.3 + - - -
63B ASN* 3.2 8.5 + - - -
65B VAL* 1.3 77.1 - - - +
67B ASP* 1.3 64.3 + - - +
69B MSE 3.2 2.5 + - + +
70B VAL* 3.1 23.4 + - - +
87B PHE* 3.5 22.3 - - + -
89B ARG* 3.0 21.6 + - - +
94B ALA* 4.0 0.2 - - - +
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 5.9 1.7 - - - +
73A ASN* 5.7 2.3 + - - -
63B ASN* 2.9 25.5 + - - +
64B ASP* 3.2 16.9 + - - +
66B THR* 1.3 78.5 - - - +
68B GLU* 1.3 62.0 + - - +
70B VAL* 3.4 3.4 - - - +
71B ARG* 3.1 52.1 + - - +
218B GLY* 4.0 13.2 - - - +
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 2.5 40.7 + - - +
64B ASP 3.0 12.2 + - - +
65B VAL* 3.6 10.2 - - - +
66B THR 3.2 0.4 - - - -
67B ASP* 1.3 74.8 - - - +
69B MSE 1.3 59.1 + - - +
71B ARG* 3.2 2.5 + - - +
72B LEU* 2.8 50.3 + - + +
82B PRO* 6.1 0.2 - - - +
96B LEU* 3.8 8.3 - - + -
216B ASP* 3.6 13.1 + - - +
217B VAL* 3.4 26.6 + - + +
218B GLY* 3.8 18.3 - - - +
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Residues in contact with MSE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 3.8 17.5 - - + -
69A MSE 3.4 33.2 - - + -
87A PHE* 4.2 1.6 - - + -
89A ARG* 4.7 11.2 - - - -
65B VAL 3.0 14.0 + - - +
66B THR 3.2 7.6 + - - +
68B GLU* 1.3 77.2 - - - +
70B VAL* 1.3 78.3 + - + +
72B LEU* 3.3 3.8 + - - -
73B ASN* 3.0 22.3 + - - -
84B ILE* 3.5 17.0 - - + +
87B PHE* 3.5 49.8 - - + -
96B LEU* 3.9 16.4 - - + -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 3.5 27.6 - - + -
67A ASP* 5.7 2.5 - - - +
70A VAL* 3.3 39.9 - - + -
141A PHE* 5.9 0.4 - - + -
66B THR 3.1 13.2 + - - +
67B ASP* 3.4 12.3 - - - +
69B MSE 1.3 83.8 - - + +
71B ARG* 1.3 71.5 + - - +
73B ASN* 3.4 6.1 + - + +
74B TRP* 3.0 28.4 + - - +
141B PHE* 3.8 16.8 - - + -
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Residues in contact with ARG 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PRO* 4.1 23.6 + - - +
141A PHE* 5.4 3.4 - - - -
67B ASP* 3.1 44.8 + - - +
68B GLU 3.9 2.0 - - - +
70B VAL* 1.3 85.3 - - - +
72B LEU* 1.3 58.6 + - - +
74B TRP* 4.0 0.6 - - - +
75B LEU* 2.9 34.7 + - - +
141B PHE* 3.5 48.2 - - + +
142B ASN 5.2 2.8 + - - -
143B SER* 5.5 1.0 + - - -
147B PHE* 6.3 0.2 - - - -
148B ARG* 5.7 2.8 - - - +
217B VAL* 3.4 23.8 - - + +
218B GLY 3.1 26.7 + - - -
219B ARG* 4.3 0.8 - - - +
220B VAL* 2.9 28.3 + - + -
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Residues in contact with LEU 72 (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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68B GLU* 2.8 44.1 + - + +
69B MSE 3.5 4.3 - - - +
71B ARG* 1.3 71.2 - - - +
73B ASN* 1.3 62.8 + - - +
76B THR* 3.1 29.6 + - - -
81B LEU* 3.8 10.5 - - + +
82B PRO* 3.8 41.6 - - + +
84B ILE* 4.0 16.2 - - + -
96B LEU* 4.0 16.6 - - + -
98B THR* 4.1 18.4 - - + -
216B ASP 5.9 0.7 - - - +
217B VAL* 3.6 23.5 - - + +
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 3.0 28.2 + - - +
66A THR* 5.0 5.7 - - - +
67A ASP* 5.9 1.4 + - - -
89A ARG* 3.5 30.2 + - - +
69B MSE 3.0 20.5 + - - +
70B VAL* 3.6 8.6 + - - +
72B LEU* 1.3 78.2 - - - +
74B TRP* 1.3 65.7 + - - +
76B THR* 3.5 16.3 - - - +
77B ALA* 4.6 1.6 + - - +
84B ILE* 3.7 17.1 - - + +
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Residues in contact with TRP 74 (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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70B VAL 3.0 17.0 + - - +
71B ARG 4.0 0.7 - - - +
73B ASN* 1.3 81.9 - - - +
75B LEU* 1.3 93.8 + - + +
76B THR 3.2 1.0 + - - -
77B ALA* 3.4 18.0 + - - +
78B PHE* 3.7 28.9 - + - -
134B ILE* 4.6 2.5 - - + -
138B ASN* 2.9 33.9 + - + -
139B CYS* 3.4 27.4 - - + -
140B PRO* 3.6 18.8 - - + +
141B PHE* 3.7 22.4 - + + -
194B VAL* 3.8 17.5 - - + -
220B VAL* 3.8 23.1 - - + -
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Residues in contact with LEU 75 (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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71B ARG 2.9 21.3 + - - +
74B TRP* 1.3 92.0 - - + +
76B THR* 1.3 60.0 + - - +
77B ALA 3.1 3.4 - - - -
78B PHE* 2.9 20.8 + - + -
79B MSE 3.0 32.3 + - + -
81B LEU* 3.6 22.4 - - + -
131B LEU* 4.0 15.5 - - + -
134B ILE* 3.8 20.2 - - + -
194B VAL* 4.7 0.7 - - + -
196B HIS* 5.6 2.0 - - + -
214B CYS* 5.0 4.0 - - - -
217B VAL* 4.4 9.0 - - + -
220B VAL* 3.8 28.7 - - + -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU 3.1 20.5 + - - +
73B ASN* 3.5 15.7 - - - +
75B LEU* 1.3 77.2 - - - +
77B ALA* 1.3 61.4 + - + +
78B PHE 3.1 1.6 + - - -
79B MSE 3.3 20.3 + - - +
81B LEU* 3.5 22.6 + - - +
82B PRO 4.7 4.6 + - - -
83B THR* 5.6 3.0 + - - -
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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
------------------------------------------------------------
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