Contacts of the helix formed by residues 77 - 93 (chain G) in PDB entry 6AHU
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 ALA 77 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A A 3.5 4.7 - - - +
33A C 4.4 10.8 - - - -
39G VAL* 3.5 27.5 - - + +
40G ASN 4.8 1.3 - - - +
41G MET* 3.7 12.3 - - + -
73G GLY* 3.8 4.5 - - - -
74G LEU* 2.9 23.6 + - - +
76G LEU* 1.3 80.0 - - - +
78G ILE* 1.3 49.7 + - - +
79G ASN 3.1 0.4 - - - -
80G ARG* 3.0 6.1 + - - +
81G ALA* 2.6 35.5 + - - +
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Residues in contact with ILE 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F THR* 4.5 5.6 + - - +
75F THR* 3.3 28.7 - - - +
78F VAL* 4.5 17.3 - - + -
73G GLY* 3.4 22.0 - - - +
74G LEU 2.7 23.7 + - - +
75G GLY* 3.4 14.4 - - - +
77G ALA* 1.3 70.6 - - - +
79G ASN* 1.3 62.9 + - - +
80G ARG 3.3 0.2 - - - -
81G ALA* 3.9 8.1 - - + -
82G ILE* 3.3 22.5 + - - +
128G SER* 3.8 22.2 - - - +
129G ALA* 4.5 1.6 - - - -
130G ILE* 3.7 34.5 - - + +
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Residues in contact with ASN 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A G 4.6 11.7 + - - +
60A U 4.7 11.5 + - - +
71F GLY 3.0 24.5 + - - +
72F ARG* 4.2 27.1 - - - +
74F THR* 3.8 9.6 - - - +
75F THR* 4.8 10.8 - - + -
133F PRO* 4.8 2.9 - - - +
76G LEU* 3.3 17.4 + - + +
77G ALA 3.1 1.0 - - - -
78G ILE* 1.3 80.3 - - - +
80G ARG* 1.3 66.0 + - + +
82G ILE* 3.4 15.4 - - - +
83G ASN* 4.3 5.2 - - - +
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Residues in contact with ARG 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A U 4.2 33.7 + - - +
39G VAL* 4.8 10.0 - - + +
40G ASN 5.3 2.7 - - - -
41G MET* 3.0 42.9 - - + +
42G LYS* 4.0 13.5 - - - +
44G ASP* 3.2 31.9 + - - +
45G PHE* 3.4 32.6 - - + +
48G GLN* 4.5 5.5 + - - +
77G ALA 3.0 5.7 + - - +
79G ASN* 1.3 85.1 - - + +
81G ALA* 1.3 61.9 + - - +
82G ILE 3.3 2.0 - - - -
83G ASN* 3.2 23.2 + - + +
84G ILE* 3.3 18.2 + - - +
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Residues in contact with ALA 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 4.4 9.4 - - + +
71G ILE* 4.1 10.1 - - + +
72G HIS 3.9 21.5 - - - +
77G ALA 2.6 22.5 + - - +
78G ILE* 4.0 12.3 - - + -
80G ARG* 1.3 72.5 - - - +
82G ILE* 1.3 62.1 + - - +
84G ILE* 3.3 25.7 - - - +
85G ALA* 3.7 3.3 + - - +
130G ILE* 5.2 1.8 - - + -
132G ILE* 3.7 15.7 - - + +
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Residues in contact with ILE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F THR* 3.5 25.8 - - + +
97F LEU* 3.7 22.0 - - + -
133F PRO* 3.7 20.2 - - + +
134F GLY 3.5 25.6 - - - +
135F LEU* 3.8 17.0 - - + -
78G ILE* 3.3 20.8 + - - +
79G ASN 3.4 13.7 - - - +
81G ALA* 1.3 77.5 - - - +
83G ASN* 1.3 64.5 + - - +
84G ILE 3.4 0.2 - - - -
85G ALA* 3.5 1.2 + - - +
86G LEU* 3.3 30.5 + - + +
130G ILE* 6.0 1.1 - - + -
132G ILE* 3.9 11.3 - - + +
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Residues in contact with ASN 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A A 3.6 23.9 + - - +
131F ASN 5.6 1.6 - - - +
133F PRO* 4.5 19.4 - - + +
45G PHE* 3.3 26.8 - - + -
79G ASN 4.3 4.7 + - - +
80G ARG* 3.2 24.1 + - - +
82G ILE* 1.3 80.7 - - - +
84G ILE* 1.3 64.5 + - - +
86G LEU* 4.5 1.4 - - - +
87G GLN* 2.9 46.8 + - - +
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Residues in contact with ILE 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 4.3 9.6 - - + -
45G PHE* 3.7 28.5 - - + -
48G GLN* 4.5 13.2 - - + +
49G LEU* 3.4 48.9 - - + +
52G CYS* 4.2 15.6 - - - -
71G ILE* 3.9 37.7 - - + -
80G ARG 3.6 8.5 - - - +
81G ALA* 3.3 24.9 - - - +
83G ASN* 1.3 76.1 - - - +
85G ALA* 1.3 62.9 + - + +
87G GLN 4.1 0.4 - - - -
88G LEU* 3.4 12.1 + - - +
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Residues in contact with ALA 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F LEU* 4.8 0.9 - - + -
71G ILE* 5.3 3.6 - - + -
81G ALA 3.7 12.1 + - - +
82G ILE 3.5 5.3 + - - +
83G ASN 3.3 0.6 - - - -
84G ILE* 1.3 86.1 - - + +
86G LEU* 1.3 69.1 + - + +
88G LEU* 3.3 21.7 + - - +
89G GLN* 3.7 14.2 + - - +
98G VAL* 5.1 5.1 - - + +
132G ILE* 3.8 31.2 - - + -
134G VAL* 5.2 6.8 - - + +
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Residues in contact with LEU 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LEU* 3.7 40.6 - - + +
98F ARG* 3.6 30.5 - - - +
99F TYR* 2.6 55.1 + - + -
133F PRO* 3.8 21.8 - - + -
134F GLY 4.2 0.9 - - - +
82G ILE* 3.3 28.5 + - + +
83G ASN* 4.7 2.0 - - - +
85G ALA* 1.3 80.2 - - + +
87G GLN* 1.3 59.4 + - + +
89G GLN* 3.4 16.0 + - + +
98G VAL* 5.8 2.2 - - + -
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Residues in contact with GLN 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A A 3.2 47.4 + - - +
65A U 5.2 3.7 - - + -
99F TYR* 4.2 5.8 - - + +
131F ASN 5.9 1.4 + - - -
45G PHE* 3.3 21.2 - - - -
49G LEU* 3.4 28.0 - - + +
83G ASN* 2.9 37.2 + - - +
84G ILE 4.5 1.1 - - - +
85G ALA 3.3 0.6 - - - -
86G LEU* 1.3 76.7 - - + +
88G LEU* 1.3 59.0 + - - +
89G GLN 3.2 0.2 - - - -
90G ALA* 3.7 3.3 + - - +
91G GLY* 3.0 24.1 + - - -
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Residues in contact with LEU 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G LEU* 4.5 8.5 - - + +
52G CYS* 4.7 19.3 - - + +
53G GLN* 4.2 22.9 - - - +
56G LEU* 4.1 30.5 - - + -
69G ILE* 4.3 18.8 - - + -
71G ILE* 5.9 2.5 - - + -
84G ILE 3.4 13.1 + - - +
85G ALA* 3.3 13.2 + - - +
86G LEU 3.2 0.6 - - - -
87G GLN* 1.3 77.3 - - - +
89G GLN* 1.3 60.9 + - - +
91G GLY* 4.3 0.9 - - - +
92G SER* 2.8 33.2 + - - +
96G LEU* 4.5 6.2 - - + +
134G VAL* 4.6 22.2 - - + -
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Residues in contact with GLN 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F TYR* 4.4 5.2 - - + +
85G ALA 3.8 13.6 + - - +
86G LEU* 3.4 13.0 + - + +
87G GLN 3.2 0.4 - - - -
88G LEU* 1.3 79.4 - - - +
90G ALA* 1.3 58.3 + - - +
93G PHE* 3.2 26.9 + - - -
94G GLY 4.0 7.3 + - - +
96G LEU* 3.0 54.6 + - - +
98G VAL* 3.4 22.6 - - + +
134G VAL* 4.6 6.1 - - - +
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Residues in contact with ALA 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A U 4.1 4.6 - - - +
99F TYR* 3.4 26.2 + - + +
87G GLN* 3.7 5.1 + - - +
89G GLN* 1.3 78.7 - - - +
91G GLY* 1.3 64.0 + - - +
93G PHE* 4.2 14.0 + - - +
68I SER* 5.6 0.9 - - - +
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Residues in contact with GLY 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A U 3.4 32.6 + - - -
53G GLN* 4.6 4.7 + - - -
87G GLN 3.0 17.1 + - - -
88G LEU* 3.8 1.6 - - - -
89G GLN 3.2 0.4 - - - -
90G ALA* 1.3 79.1 - - - +
92G SER* 1.3 62.1 + - - +
93G PHE* 3.5 4.3 + - - +
68I SER* 4.1 14.9 + - - -
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Residues in contact with SER 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E LEU* 3.5 28.0 - - - +
53G GLN* 4.5 12.9 + - - +
56G LEU* 4.3 9.8 - - - +
57G ASP* 5.6 1.7 + - - -
88G LEU* 2.8 30.2 + - - -
91G GLY* 1.3 69.2 - - - -
93G PHE* 1.3 59.4 + - - +
94G GLY* 2.9 14.1 + - - -
96G LEU* 3.7 25.2 - - - +
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Residues in contact with PHE 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E LEU* 3.2 32.4 - - + +
124E ILE* 3.9 26.5 - - + -
126E LEU* 5.0 3.0 - - + +
127E GLN* 3.2 39.5 - - + -
128E ASN* 5.6 0.9 - - - -
89G GLN 3.2 19.1 + - - -
90G ALA* 4.4 10.8 - - - +
91G GLY 3.3 7.6 - - - +
92G SER* 1.3 77.0 - - - +
94G GLY* 1.3 59.4 + - - +
61I LEU* 6.6 0.4 - - + -
63I ILE* 4.5 22.2 - - + -
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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
------------------------------------------------------------
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