Contacts of the strand formed by residues 171 - 175 (chain G) in PDB entry 3CII
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 ARG 171 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.3 27.7 - - - +
76G SER* 3.2 30.9 + - - +
77G SER 3.6 15.9 + - - -
78G GLU 3.5 8.5 - - - +
79G GLN* 3.7 18.1 + - - +
113G GLN* 3.0 50.5 + - + +
114G PHE 3.3 14.3 + - - +
115G TYR* 3.5 20.2 - - + -
116G TRP* 3.1 18.2 + - - -
170G ASN* 1.3 79.7 - - - +
172G TYR* 1.3 57.7 + - - +
164H LYS* 3.1 29.5 - - - +
168H ILE* 4.0 11.9 - - - +
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Residues in contact with TYR 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G PHE* 3.6 17.2 - + - +
76G SER* 3.1 53.1 + - - -
78G GLU* 3.8 17.5 + - - -
80G LYS* 3.8 25.1 - - + -
85G SER* 3.8 24.9 - - - -
88G LEU* 4.0 21.7 - - + +
89G CYS* 4.1 12.8 - - - -
92G GLN* 5.4 1.2 + - - -
96G LEU* 4.3 1.8 - - + -
115G TYR* 3.4 4.8 - - - -
116G TRP* 3.8 26.2 - + + +
170G ASN 4.2 7.4 - - - -
171G ARG* 1.3 77.0 - - - +
173G ILE* 1.3 68.1 + - - +
174G CYS* 3.9 21.0 - - - -
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Residues in contact with ILE 173 (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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73G TYR* 4.5 12.3 - - + -
74G PHE 3.2 12.6 - - - +
75G ILE* 4.7 6.3 - - + +
96G LEU* 3.2 12.7 - - - +
97G LEU* 3.0 61.9 + - + +
105G LEU* 3.7 19.5 - - + -
108G MET* 3.9 20.0 - - + -
115G TYR* 3.8 24.5 - - + -
116G TRP 3.8 6.0 + - - +
172G TYR* 1.3 78.9 - - - +
174G CYS* 1.3 77.5 + - - +
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Residues in contact with CYS 174 (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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65G TRP* 3.9 14.6 - - + -
73G TYR* 3.6 2.9 - - - -
74G PHE* 3.0 41.1 + - + -
88G LEU 4.7 1.3 - - - -
89G CYS* 2.0 48.5 - - - -
92G GLN* 5.3 1.8 - - - -
94G SER* 3.0 19.1 - - - +
95G SER 3.3 6.3 - - - -
97G LEU 4.8 0.4 - - - -
172G TYR* 3.9 15.7 - - - -
173G ILE* 1.3 83.1 - - - +
175G LYS* 1.3 59.0 + - - +
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Residues in contact with LYS 175 (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 ASN* 3.2 12.6 - - - +
72G CYS 3.5 4.0 - - - -
73G TYR* 3.7 19.5 - - + -
94G SER* 3.4 6.3 - - - -
95G SER* 2.8 39.3 + - - +
97G LEU* 4.2 13.0 - - + -
98G GLN* 3.8 25.0 + - + +
100G GLN* 3.2 23.0 + - - -
104G GLU* 3.1 24.9 - - - +
174G CYS* 1.3 78.1 - - - +
176G GLN* 1.3 69.2 + - - +
177G GLN* 3.1 28.4 + - - +
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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