Contacts of the strand formed by residues 84 - 88 (chain P) in PDB entry 1SVC
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 GLN 84 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P ILE* 3.4 6.8 - - - +
48P LEU* 2.7 54.1 + - + +
49P GLU* 2.7 38.2 + - + +
81P SER* 6.1 0.2 - - - +
82P TYR* 3.2 19.6 + - + +
83P PRO* 1.3 74.0 - - - +
85P VAL* 1.3 63.0 + - - +
134P VAL* 4.1 10.5 - - + +
135P VAL 4.4 2.5 - - - -
136P GLY* 4.1 13.6 - - - +
137P PHE* 5.2 0.2 - - - -
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Residues in contact with VAL 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P LEU* 3.3 31.9 - - + -
46P GLN 3.3 15.5 - - - +
47P ILE* 4.5 4.5 - - + -
48P LEU* 3.8 2.5 - - - +
83P PRO 5.8 0.2 - - - -
84P GLN* 1.3 78.8 - - - +
86P LYS* 1.3 75.6 + - - +
87P ILE* 5.0 0.7 - - + +
96P VAL* 4.7 9.9 - - + -
134P VAL* 3.6 9.9 - - - +
135P VAL* 3.5 32.3 + - + +
137P PHE* 3.9 7.6 - - + -
217P PHE* 3.6 46.4 - - + -
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Residues in contact with LYS 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P LEU* 3.5 0.7 - - - -
46P GLN* 2.7 51.4 + - - +
48P LEU* 3.6 26.4 - - + +
85P VAL* 1.3 79.3 - - - +
87P ILE* 1.3 67.7 + - - +
88P CYS* 3.2 34.1 + - - +
133P MET* 3.9 8.8 - - + +
134P VAL* 3.9 21.3 - - + +
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Residues in contact with ILE 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P PRO* 5.4 2.0 - - + -
44P TYR 3.9 2.7 - - - -
45P LEU* 4.4 4.0 - - + +
85P VAL* 5.5 0.7 - - + -
86P LYS* 1.3 74.4 - - - +
88P CYS* 1.3 65.5 + - - +
89P ASN 3.7 1.2 + - - -
90P TYR 4.2 2.0 + - - +
91P VAL* 4.8 9.6 - - + +
94P ALA* 3.2 33.0 - - + -
96P VAL* 4.4 14.1 - - + -
128P ALA* 3.9 20.4 - - + -
133P MET* 3.2 41.8 + - + +
135P VAL* 6.2 0.2 - - + -
219P ALA* 4.3 17.7 - - + -
221P LEU* 4.5 10.5 - - + -
232P LEU* 4.4 19.3 - - + -
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Residues in contact with CYS 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P PRO* 3.5 3.3 - - - +
44P TYR* 2.8 65.5 + - + +
46P GLN* 3.6 23.8 - - - -
86P LYS* 3.2 41.5 + - - +
87P ILE* 1.3 74.0 - - - +
89P ASN* 1.3 69.0 + - - +
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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