Contacts of the helix formed by residues 77 - 87 (chain G) in PDB entry 6C6U
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 ASP 77 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69G SER 4.5 6.3 - - - +
70G THR* 3.7 6.9 - - - +
76G GLU* 1.3 78.3 - - - +
78G ILE* 1.3 68.7 + - - +
79G LEU* 3.2 8.7 - - + +
80G GLU* 3.4 12.4 + - + +
81G ILE* 3.2 21.5 + - - +
729I ALA* 3.6 13.8 - - - +
755I LYS* 2.8 39.4 + - - -
756I TYR* 3.7 15.0 + - + +
766I ASN* 3.6 15.4 + - - -
768I MET* 4.4 11.3 - - + +
769I PRO* 5.9 0.6 - - - +
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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
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61G ILE* 3.7 30.5 - - + -
64G VAL* 3.7 33.2 - - + -
67G GLU 3.8 13.9 - - - +
69G SER* 3.7 23.6 + - - +
71G LYS* 4.1 22.2 - - + +
76G GLU 5.2 1.1 - - - +
77G ASP* 1.3 75.2 - - - +
79G LEU* 1.3 57.8 + - - +
81G ILE* 3.3 23.1 + - + +
82G LEU* 3.0 27.8 + - - +
171G LEU* 3.8 17.3 - - + -
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Residues in contact with LEU 79 (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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67G GLU* 3.5 16.0 + - + +
68G TYR* 4.1 17.9 - - + -
77G ASP* 3.2 4.3 - - + +
78G ILE* 1.3 78.4 - - - +
80G GLU* 1.3 59.3 + - + +
82G LEU* 3.2 12.6 + - + +
83G LEU* 3.0 40.1 + - + +
693I LEU* 3.7 34.1 - - + +
694I ARG* 5.6 2.2 - - - +
756I TYR* 3.7 26.2 - - + +
831I ILE* 3.8 22.7 - - + -
1057I LYS* 4.5 14.8 - - - +
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Residues in contact with GLU 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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76G GLU* 3.4 41.2 - - + +
77G ASP* 3.4 14.7 + - + +
78G ILE 3.3 0.4 - - - -
79G LEU* 1.3 78.1 - - + +
81G ILE* 1.3 61.0 + - - +
83G LEU* 3.2 4.3 + - + +
84G ASN* 2.9 46.2 + - - +
694I ARG* 3.3 35.7 + - - +
768I MET* 3.3 24.8 - - + +
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Residues in contact with ILE 81 (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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61G ILE* 4.9 9.9 - - + -
74G VAL* 4.1 17.0 - - + -
76G GLU* 4.4 4.7 - - + +
77G ASP 3.2 16.8 + - - +
78G ILE* 3.5 28.7 - - + +
80G GLU* 1.3 76.6 - - - +
82G LEU* 1.3 57.3 + - - +
84G ASN* 3.4 6.6 + - - +
85G LEU* 2.9 35.5 + - + +
130G ILE* 3.8 17.5 - - + -
131G CYS* 3.8 30.7 - - + -
140G ILE* 5.6 4.0 - - + -
142G MET* 4.1 21.5 - - + -
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Residues in contact with LEU 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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59G VAL* 3.8 25.6 - - + -
61G ILE* 4.5 3.4 - - + -
67G GLU* 3.3 32.3 - - + +
78G ILE 3.0 17.9 + - - +
79G LEU* 3.2 12.7 + - + +
81G ILE* 1.3 77.4 - - - +
83G LEU* 1.3 60.0 + - + +
85G LEU* 3.4 3.9 + - + +
86G LYS* 2.9 28.3 + - - +
171G LEU* 3.7 33.7 - - + -
172G LEU 5.0 1.6 - - - +
173G VAL* 3.7 32.8 - - + +
1057I LYS* 6.1 0.4 - - - +
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Residues in contact with LEU 83 (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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79G LEU* 3.0 41.9 + - + +
80G GLU* 3.2 8.7 + - + +
82G LEU* 1.3 79.2 - - + +
84G ASN* 1.3 63.3 + - - +
86G LYS* 3.0 16.5 + - + +
87G GLY* 3.0 19.9 + - - -
693I LEU* 3.8 26.0 - - + -
694I ARG* 4.2 23.6 - - + +
825I GLU 5.7 2.9 - - - +
826I ASP* 5.4 14.6 - - + +
1057I LYS* 5.9 2.0 - - - +
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Residues in contact with ASN 84 (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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76G GLU* 3.4 13.9 + - - -
80G GLU* 2.9 30.8 + - - +
81G ILE 3.9 3.8 - - - +
83G LEU* 1.3 76.8 - - - +
85G LEU* 1.3 61.7 + - - +
87G GLY* 3.6 6.0 + - - +
88G LEU* 4.0 0.5 + - - +
128G HIS* 3.0 31.5 + - - -
129G VAL* 4.0 12.4 - - - +
130G ILE* 2.7 40.0 + - - +
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Residues in contact with LEU 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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56G VAL* 3.3 19.3 - - + +
59G VAL* 3.8 33.7 - - + -
81G ILE* 2.9 28.3 + - + +
82G LEU* 3.9 4.3 - - - +
84G ASN* 1.3 74.8 - - - +
86G LYS* 1.3 64.6 + - - +
87G GLY 3.2 0.4 - - - -
88G LEU* 3.2 30.8 + - + +
102G LEU* 5.4 1.1 - - + -
115G ILE* 5.8 0.4 - - + -
130G ILE* 3.7 30.7 - - + -
142G MET* 3.7 25.1 - - - -
144G ILE* 3.9 23.8 - - + -
173G VAL* 5.9 0.4 - - + -
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Residues in contact with LYS 86 (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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55G ALA* 5.5 5.2 - - - +
56G VAL* 3.9 14.2 - - + +
82G LEU 2.9 14.3 + - - +
83G LEU* 3.0 19.5 + - + +
85G LEU* 1.3 77.4 - - - +
87G GLY* 1.3 56.2 + - - +
88G LEU 3.2 6.8 + - - +
152G TYR* 5.3 1.3 - - - -
173G VAL* 4.9 6.0 - - + +
174G ASP* 4.1 36.8 - - + +
176G CYS* 4.4 22.4 - - + +
824I GLN 3.3 21.1 + - - -
825I GLU* 5.0 3.4 - - - +
826I ASP* 3.4 27.1 - - + +
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Residues in contact with GLY 87 (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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83G LEU 3.0 12.2 + - - -
84G ASN* 3.6 8.6 + - - -
85G LEU 3.2 0.8 - - - -
86G LYS* 1.3 75.9 - - - +
88G LEU* 1.3 59.0 + - - -
89G ALA* 3.6 4.3 + - - +
128G HIS* 3.9 18.6 + - - -
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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