Contacts of the helix formed by residues 89 - 102 (chain G) in PDB entry 6CP3
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 SER 89 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398F GLU* 3.2 26.6 + - - -
401F LYS* 4.7 15.3 + - - -
85G GLY 5.3 0.6 + - - -
86G SER* 5.5 2.7 - - - +
87G ILE 4.5 1.4 - - - +
88G HIS* 1.3 79.1 + - - +
90G GLN* 1.3 61.8 + - - +
91G LEU 3.5 0.4 - - - -
92G ALA* 3.9 7.5 - - - +
93G LYS* 3.0 27.9 + - - +
117G GLN* 4.5 5.1 + - - -
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Residues in contact with GLN 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G SER* 3.7 23.1 + - - +
87G ILE* 3.2 6.0 + - - +
89G SER* 1.3 78.6 - - - +
91G LEU* 1.3 57.7 + - - +
93G LYS* 3.1 12.4 + - - +
94G ALA* 3.0 25.1 + - - +
97G ARG* 5.1 14.6 - - - +
175G PHE* 3.6 28.5 - - + -
177G PRO* 3.8 23.3 - - + +
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Residues in contact with LEU 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G ALA* 4.3 10.5 - - + -
77G ILE 4.2 2.7 - - - +
78G THR* 3.7 28.9 - - + -
87G ILE 3.2 11.4 + - - +
90G GLN* 1.3 75.5 - - - +
92G ALA* 1.3 60.9 + - - +
94G ALA* 3.3 5.7 + - + +
95G VAL* 2.9 29.7 + - + +
114G ILE* 4.4 2.2 - - + -
165G PHE* 3.7 44.4 - - + +
166G TYR 4.2 3.6 - - - +
167G ASN* 3.4 28.5 - - - +
177G PRO* 3.7 22.0 - - + -
178G SER 4.9 0.4 - - - +
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Residues in contact with ALA 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G HIS 3.7 18.5 + - - +
89G SER* 3.7 8.2 + - - +
91G LEU* 1.3 78.1 - - - +
93G LYS* 1.3 58.4 + - - +
95G VAL* 3.3 8.2 + - - +
96G ARG* 2.9 31.4 + - - +
114G ILE* 3.7 21.3 - - + +
117G GLN* 4.2 17.7 - - + +
118G LEU* 4.4 6.1 - - + +
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Residues in contact with LYS 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G SER 3.0 18.8 + - - +
90G GLN* 3.1 12.9 + - - +
92G ALA* 1.3 74.9 - - - +
94G ALA* 1.3 60.7 + - - +
96G ARG* 3.1 10.8 + - + +
97G ARG* 3.0 71.9 + - - +
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Residues in contact with ALA 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G GLN 3.0 13.1 + - - +
91G LEU* 3.3 11.8 + - + +
93G LYS* 1.3 74.7 - - - +
95G VAL* 1.3 64.4 + - - +
97G ARG* 3.4 18.6 + - - +
98G HIS* 3.0 26.2 + - - +
165G PHE* 3.9 10.1 - - + -
177G PRO* 4.2 24.2 - - + -
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Residues in contact with VAL 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ILE* 4.8 9.8 - - + +
76G ALA* 4.7 16.2 - - + -
91G LEU* 2.9 19.6 + - + +
92G ALA* 3.4 11.9 - - - +
94G ALA* 1.3 75.1 - - - +
96G ARG* 1.3 52.1 + - - +
98G HIS* 3.7 0.9 - - - +
99G LEU* 2.6 57.3 + - + +
107G ILE* 4.7 4.0 - - + -
114G ILE* 5.4 0.9 - - + -
118G LEU* 3.7 33.7 - - + -
165G PHE* 3.6 27.6 - - + -
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Residues in contact with ARG 96 (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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92G ALA* 2.9 18.0 + - - +
93G LYS* 3.1 15.4 + - + +
95G VAL* 1.3 78.4 - - - +
97G ARG* 1.3 62.3 + - + +
99G LEU* 4.2 7.0 - - - +
100G ASN* 3.0 51.0 + - - +
120G ARG* 4.8 8.1 - - - +
121G THR* 3.1 42.5 + - - +
122G HIS* 4.3 15.9 + - - -
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Residues in contact with ARG 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G GLN* 5.1 11.1 - - - +
93G LYS* 3.0 54.2 + - - +
94G ALA* 3.8 22.2 - - - +
96G ARG* 1.3 78.8 - - + +
98G HIS* 1.3 61.7 + - - +
99G LEU 3.3 0.7 + - - -
100G ASN* 3.8 10.4 + - - +
101G ASP* 3.7 16.3 + - - +
177G PRO* 6.1 1.2 - - - +
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Residues in contact with HIS 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G GLU* 3.3 31.3 + - - -
74G ILE* 3.5 26.7 - - + +
94G ALA 3.0 17.3 + - - +
95G VAL 4.1 0.9 - - - +
97G ARG* 1.3 77.5 - - - +
99G LEU* 1.3 58.8 + - - +
100G ASN 3.6 0.2 - - - -
101G ASP* 3.6 11.7 + - + +
102G GLN* 3.0 36.8 + - - +
161G LYS* 5.0 6.1 - - - -
163G SER* 4.1 4.8 + - - -
165G PHE* 3.7 22.2 - + + -
179G GLU* 3.8 27.6 + - - +
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Residues in contact with LEU 99 (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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74G ILE* 3.8 20.2 - - + -
95G VAL* 2.6 30.7 + - + +
96G ARG* 3.9 7.4 - - - +
97G ARG 3.2 0.2 - - - -
98G HIS* 1.3 76.5 - - - +
100G ASN* 1.3 65.3 + - - +
101G ASP 3.1 1.6 - - - -
102G GLN 3.2 32.1 - - - +
103G PRO* 3.3 8.9 - - + +
105G ALA 4.4 6.7 - - - +
107G ILE* 3.7 34.5 - - + -
118G LEU* 5.1 2.7 - - + -
121G THR* 6.4 0.2 - - + -
122G HIS* 4.4 22.9 - - + +
125G ASN* 4.0 15.7 - - - +
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Residues in contact with ASN 100 (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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96G ARG* 3.0 44.1 + - - +
97G ARG* 4.3 6.7 - - - +
98G HIS 3.6 0.2 - - - -
99G LEU* 1.3 76.2 - - - +
101G ASP* 1.3 65.3 + - - +
103G PRO* 4.1 10.8 - - - +
122G HIS* 5.6 4.5 + - - -
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Residues in contact with ASP 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G ARG 3.7 15.1 - - - +
98G HIS* 3.6 9.2 + - - +
99G LEU 3.1 1.0 - - - -
100G ASN* 1.3 82.3 - - - +
102G GLN* 1.3 85.5 + - - +
103G PRO* 3.6 5.8 - - - +
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Residues in contact with GLN 102 (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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71G LYS 6.3 0.7 - - - +
72G GLU* 3.6 28.3 + - + +
74G ILE* 5.9 0.2 - - + -
98G HIS* 3.0 35.0 + - + +
99G LEU* 3.2 14.3 + - - +
101G ASP* 1.3 93.6 + - - +
103G PRO* 1.3 65.4 - - - +
104G ASN* 3.2 12.5 + - - +
105G ALA* 3.2 22.0 + - + +
161G LYS* 6.1 2.8 - - - +
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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