Contacts of the strand formed by residues 1076 - 1079 (chain C) in PDB entry 7C17
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 ILE1076 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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816C ILE* 3.7 15.7 - - + +
818C VAL* 3.7 37.2 - - + -
1060C ILE* 4.5 7.4 - - + +
1061C GLN 3.4 27.8 - - - +
1062C PRO* 3.3 9.0 - - + -
1063C GLY 2.9 23.1 + - - +
1064C ASP* 3.0 26.6 + - + +
1066C MET* 3.7 33.9 - - + -
1075C VAL* 1.3 69.9 - - - +
1077C SER* 1.3 63.6 + - - +
1078C LYS 4.4 5.6 - - - +
1079C ILE* 4.7 1.1 - - + -
356D THR* 3.3 8.3 - - - +
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Residues in contact with SER1077 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810C TYR* 3.2 41.9 + - - -
815C SER* 3.6 8.0 + - - -
816C ILE 3.0 16.2 + - - -
817C LEU* 4.8 1.6 - - - -
1062C PRO* 4.0 7.4 - - - +
1075C VAL 3.1 1.3 + - - -
1076C ILE* 1.3 75.2 - - - +
1078C LYS* 1.3 64.2 + - - +
356D THR* 4.2 16.0 + - - -
357D VAL* 3.4 22.4 + - - +
448D GLN* 3.7 16.1 + - - +
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Residues in contact with LYS1078 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ASP* 5.5 12.1 - - - +
810C TYR* 3.7 29.2 - - + +
817C LEU* 3.5 16.9 - - + +
818C VAL* 3.7 11.4 + - - +
1062C PRO* 4.4 17.8 - - + +
1076C ILE* 3.6 2.2 - - - -
1077C SER* 1.3 84.4 - - - +
1079C ILE* 1.3 90.0 + - - +
1080C ASN* 3.0 16.9 + - - +
1081C PRO* 6.1 0.7 - - + -
360D TYR* 5.4 5.6 - - + +
442D ILE* 6.5 0.4 - - + -
443D GLU* 4.8 17.4 - - - +
448D GLN* 4.4 10.8 - - - +
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Residues in contact with ILE1079 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 6.0 1.0 - - - -
818C VAL* 3.9 12.1 - - + -
819C SER 3.6 16.6 - - - +
820C GLU* 3.4 32.0 - - - +
822C VAL* 6.2 0.2 - - + -
823C VAL* 4.4 17.5 - - + -
1059C ARG* 6.4 0.4 - - + -
1060C ILE 3.3 26.2 - - - +
1061C GLN* 4.4 2.2 - - + -
1062C PRO* 3.7 27.4 - - + +
1076C ILE* 4.7 0.9 - - + -
1078C LYS* 1.3 92.5 - - - +
1080C ASN* 1.3 60.9 + - - +
1081C PRO* 3.8 4.3 - - - +
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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