Contacts of the helix formed by residues 89 - 103 (chain H) in PDB entry 3GHG
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 GLN 89 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G LYS* 5.4 1.1 + - - +
55G ILE* 4.4 2.0 - - - +
56G ASP* 4.6 6.8 + - - +
59G ASN* 2.8 50.0 + - + +
63G THR* 6.5 0.2 - - + -
85H ALA 2.6 28.8 + - - +
86H LEU* 2.9 19.3 + - - +
88H GLN* 1.3 79.3 - - + +
90H GLU* 1.3 58.2 + - - +
92H PRO* 3.5 11.9 - - + -
93H ILE* 3.4 32.5 + - + +
32I TYR* 4.4 3.0 + - - -
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Residues in contact with GLU 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H LEU* 3.7 6.3 + - + +
87H LEU* 3.2 41.3 + - - +
89H GLN* 1.3 77.8 - - - +
91H ARG* 1.3 63.4 + - + +
92H PRO 3.3 0.2 - - - -
93H ILE* 5.0 0.4 - - - -
94H ARG* 2.9 66.1 + - - +
28I PHE* 3.9 23.2 - - - -
32I TYR* 4.2 27.3 - - + +
14L ARG* 4.8 2.3 + - - -
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Residues in contact with ARG 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H GLU* 5.8 1.6 + - - -
87H LEU* 3.7 28.3 + - + +
88H GLN* 3.4 41.9 + - - +
90H GLU* 1.3 78.8 - - + +
92H PRO* 1.4 60.6 - - + +
94H ARG* 5.0 0.4 - - - -
95H ASN* 3.0 37.9 + - - +
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Residues in contact with PRO 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H GLN 3.1 26.5 - - - +
89H GLN* 3.5 13.7 - - + +
90H GLU 3.6 0.9 - - - -
91H ARG* 1.4 91.7 - - + +
93H ILE* 1.3 72.4 + - + +
95H ASN* 3.0 15.2 + - + +
96H SER* 3.0 15.5 + - - -
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Residues in contact with ILE 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ASN* 4.0 17.7 - - + +
62G PHE* 3.5 39.0 - - + +
63G THR* 4.5 19.7 - - + -
66G ILE* 5.3 6.5 - - + +
89H GLN* 3.4 22.3 + - + +
90H GLU 4.6 0.7 - - - +
92H PRO* 1.3 84.0 - - + +
94H ARG* 1.3 58.7 + - - +
96H SER* 3.1 24.2 + - - -
97H VAL* 3.1 17.0 + - + +
32I TYR* 4.8 10.1 - - + +
36I VAL* 4.5 20.6 - - + -
40I LEU* 6.3 0.4 - - + -
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Residues in contact with ARG 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H GLU* 2.9 52.4 + - + +
91H ARG* 5.0 0.9 - - - -
93H ILE* 1.3 78.7 - - - +
95H ASN* 1.3 67.2 + - - +
97H VAL* 3.6 13.7 - - + +
98H ASP* 3.4 18.0 + - - +
32I TYR* 3.9 24.7 - - + +
36I VAL* 5.4 7.4 - - + -
14L ARG* 4.5 17.4 - - - +
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Residues in contact with ASN 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ARG* 3.0 24.1 + - - +
92H PRO* 3.0 4.3 + - + +
94H ARG* 1.3 85.7 + - - +
96H SER* 1.3 60.0 + - - +
97H VAL 3.3 1.6 - - - -
98H ASP* 3.4 13.7 - - + +
99H GLU* 3.0 29.0 + - - +
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Residues in contact with SER 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ILE* 3.7 29.0 - - - +
70G LYS* 5.9 2.8 + - - -
92H PRO* 3.0 17.3 + - - +
93H ILE* 3.1 10.1 + - - -
95H ASN* 1.3 72.6 - - - +
97H VAL* 1.3 67.4 + - - +
99H GLU* 3.4 10.7 - - - +
100H LEU* 2.9 34.0 + - - +
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Residues in contact with VAL 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ILE* 4.8 3.1 - - + +
93H ILE* 3.1 16.8 + - + +
94H ARG* 3.6 18.2 - - + +
96H SER* 1.3 77.6 - - - +
98H ASP* 1.3 66.2 + - - +
100H LEU* 3.5 3.7 - - - -
101H ASN* 2.8 45.0 + - - +
36I VAL* 4.9 16.2 - - + -
39I ASP* 4.4 16.4 - - + +
40I LEU* 4.0 26.0 - - + -
43I LEU* 4.2 5.1 - - + +
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Residues in contact with ASP 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H ARG 3.4 5.8 + - - +
95H ASN* 3.3 22.3 + - - +
96H SER 3.3 0.4 - - - -
97H VAL* 1.3 80.4 - - - +
99H GLU* 1.3 65.5 + - - +
101H ASN* 3.1 11.4 + - - +
102H ASN* 2.6 55.2 + - - -
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Residues in contact with GLU 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G LYS* 4.7 12.5 - - - +
95H ASN 3.0 16.6 + - - +
96H SER* 3.4 14.7 - - - +
98H ASP* 1.3 80.5 - - - +
100H LEU* 1.3 82.1 + - - +
101H ASN 3.1 0.2 - - - -
102H ASN* 2.9 10.6 + - - +
103H ASN* 2.4 49.6 + - + +
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Residues in contact with LEU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ILE* 3.5 37.0 - - + -
69G LEU* 3.4 32.5 - - + -
70G LYS* 4.2 16.4 - - + -
73G LEU* 4.1 22.0 - - + -
96H SER* 2.9 18.0 + - - +
97H VAL* 4.8 0.4 - - - -
99H GLU* 1.3 99.9 + - - +
101H ASN* 1.3 58.3 + - - +
103H ASN* 3.7 5.6 - - + -
104H VAL* 3.1 22.9 - - + +
43I LEU* 3.1 26.4 - - + +
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Residues in contact with ASN 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H VAL* 2.8 42.4 + - - +
98H ASP* 3.3 9.5 - - - +
100H LEU* 1.3 77.4 - - - +
102H ASN* 1.3 61.3 + - - +
103H ASN 3.1 1.3 - - - -
105H GLU* 3.2 42.8 + - + +
106H ALA 3.7 1.2 + - - -
39I ASP* 5.2 1.8 + - - +
43I LEU* 3.0 30.8 - - - +
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Residues in contact with ASN 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H ASP* 2.6 44.7 + - - -
99H GLU* 2.9 11.7 + - - +
101H ASN* 1.3 77.9 - - - +
103H ASN* 1.3 59.3 + - - +
104H VAL 3.6 0.4 - - - -
106H ALA* 3.2 29.0 - - + +
107H VAL* 3.3 9.0 - - - +
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Residues in contact with ASN 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G LEU* 3.0 37.6 - - - +
74G PHE* 5.3 2.1 - - - -
77G GLN* 2.9 26.2 + - - +
99H GLU* 2.4 41.0 + - - +
100H LEU* 3.9 5.8 - - + -
101H ASN 3.1 0.4 - - - -
102H ASN* 1.3 76.2 + - - +
104H VAL* 1.3 59.1 + - - +
107H VAL* 3.5 27.7 - - - +
108H SER 4.7 0.5 + - - -
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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