Contacts of the strand formed by residues 71 - 75 (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 ASN 71 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61G CYS* 4.0 1.6 - - - -
66G VAL 3.6 0.2 - - - +
67G GLY* 3.3 7.3 - - - -
68G TYR 2.8 35.9 + - - +
69G ARG* 3.5 13.3 + - - +
70G CYS* 1.3 80.5 - - - +
72G CYS* 1.3 62.5 + - - +
73G TYR* 3.1 34.4 + - + -
100G GLN* 6.0 0.4 - - - +
104G GLU* 3.7 4.9 + - - +
175G LYS* 3.2 21.4 - - - +
176G GLN 3.7 14.6 - - - +
177G GLN* 3.4 20.4 + - - +
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Residues in contact with CYS 72 (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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60G SER 3.7 7.0 - - - -
61G CYS* 2.0 57.7 - - + -
62G GLN* 4.2 3.8 - - - -
65G TRP* 3.9 16.0 - - + -
71G ASN* 1.3 71.5 - - - +
73G TYR* 1.3 62.3 + - - +
175G LYS* 3.5 4.0 - - - -
176G GLN* 2.7 59.3 + - + +
177G GLN 4.4 3.7 + - - +
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Residues in contact with TYR 73 (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* 3.3 10.7 - - - -
66G VAL* 2.7 54.3 + - + +
68G TYR* 3.9 25.5 + + + -
69G ARG* 4.9 2.8 - - - +
71G ASN* 3.1 24.5 + - + +
72G CYS* 1.3 75.3 - - - +
74G PHE* 1.3 59.3 + - - +
75G ILE* 5.0 2.9 - - + -
97G LEU* 4.8 2.9 - - + -
104G GLU* 3.0 47.0 + - - +
105G LEU* 4.5 9.4 - - + -
107G PHE* 4.1 21.5 - + + -
173G ILE* 4.5 12.1 - - + -
174G CYS 3.6 11.9 - - - +
175G LYS* 3.7 26.0 - - + -
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Residues in contact with PHE 74 (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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64G LYS* 3.8 43.7 - - + -
65G TRP* 3.2 39.0 - + + -
73G TYR* 1.3 71.4 - - - +
75G ILE* 1.3 74.9 + - - +
76G SER* 5.2 2.9 - - - -
77G SER* 5.1 8.3 - - - -
78G GLU* 5.4 5.8 - - - -
92G GLN* 3.9 23.8 - - - -
172G TYR* 3.6 21.7 - + - +
173G ILE* 3.2 9.0 - - - -
174G CYS* 3.0 47.3 + - + -
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Residues in contact with ILE 75 (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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64G LYS 5.6 0.6 + - - +
66G VAL* 3.9 27.3 - - + +
73G TYR* 4.0 4.9 + - + -
74G PHE* 1.3 92.4 - - - +
76G SER* 1.3 66.6 + - - +
77G SER* 4.0 1.7 + - - -
107G PHE* 4.5 2.2 - - + -
108G MET* 3.9 26.9 - - + -
115G TYR* 3.4 34.1 - - + +
172G TYR 4.0 2.0 - - - -
173G ILE* 4.7 8.1 - - + -
165H PHE* 5.2 6.5 - - + -
168H ILE* 3.7 20.4 - - + -
169H ILE* 4.0 20.2 - - + -
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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
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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