Contacts of the strand formed by residues 92 - 97 (chain P) in PDB entry 1SXG
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 92 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F HIS* 3.2 34.7 + - + -
108F LEU* 6.1 4.0 - - + -
111F ASN* 3.3 12.9 + - - +
60P THR* 4.0 14.6 - - - +
61P THR 3.5 6.4 + - - +
62P THR* 3.3 33.7 + - - +
63P VAL* 3.3 26.6 + - - +
90P LYS 5.7 0.4 + - - -
91P TYR* 1.3 78.8 - - - +
93P ILE* 1.3 63.5 + - - +
94P ILE 4.3 0.2 - - - -
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Residues in contact with ILE 93 (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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96F SER* 3.4 27.1 - - - -
97F ASN 5.7 0.7 - - - +
108F LEU* 5.3 3.2 - - + +
63P VAL* 3.5 29.6 - - + +
65P VAL* 4.0 15.3 - - + -
82P ILE* 3.7 22.7 - - + +
83P GLU* 2.7 46.4 - - - +
86P ALA* 3.6 23.1 - - + -
92P ASN* 1.3 77.5 - - - +
94P ILE* 1.3 62.7 + - - +
95P LEU* 3.8 5.5 + - + -
302P MET* 4.8 0.2 - - + -
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Residues in contact with ILE 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F ILE* 3.3 48.9 - - + -
95F LEU 4.3 1.1 - - - -
96F SER* 5.2 1.1 - - - -
115F LYS* 4.9 14.6 - - + +
62P THR* 4.1 10.6 + - - +
63P VAL 3.1 5.7 + - - +
64P GLY* 3.1 20.2 - - - -
65P VAL* 3.0 21.0 + - - +
92P ASN 4.3 0.2 - - - -
93P ILE* 1.3 73.3 - - - +
95P LEU* 1.3 63.0 + - - +
96P SER* 3.8 4.3 - - - +
112P MET* 3.5 21.5 - - + -
115P LYS* 5.4 3.6 - - + -
117P VAL* 3.7 22.0 - - + -
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Residues in contact with LEU 95 (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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70F ILE* 4.9 4.3 - - + -
93F ILE 3.9 0.5 - - - +
94F ILE* 3.9 0.5 - - - -
95F LEU* 2.9 62.1 + - + +
96F SER* 5.3 0.4 - - - -
97F ASN* 4.6 14.6 - - - +
65P VAL* 3.3 30.7 - - + -
67P ILE* 4.3 9.6 - - + -
70P ILE* 4.0 22.0 - - + -
79P ALA* 4.0 22.4 - - + +
83P GLU* 5.1 8.5 - - - +
93P ILE* 4.8 4.9 - - + +
94P ILE* 1.3 77.2 - - - +
96P SER* 1.3 68.6 + - - +
97P ASN* 4.7 0.9 - - + +
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Residues in contact with SER 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ILE 3.5 17.6 + - - -
94F ILE* 4.1 1.7 - - - +
95F LEU* 5.9 0.2 - - - -
65P VAL 3.0 7.3 + - - +
66P ILE* 3.3 27.0 - - - +
67P ILE* 3.1 25.3 + - - +
94P ILE* 3.8 3.2 - - - +
95P LEU* 1.3 78.4 - - - +
97P ASN* 1.3 60.3 + - - +
108P LEU* 3.8 19.4 - - - +
112P MET* 3.1 23.0 - - - +
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Residues in contact with ASN 97 (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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80F ARG* 6.4 0.2 - - - +
83F GLU* 3.6 35.6 + - - +
93F ILE* 6.0 0.4 - - - +
67P ILE* 3.3 22.4 - - + +
68P PRO 2.6 26.2 - - - +
69P ASP* 3.6 1.7 + - - -
70P ILE* 3.4 23.8 + - + +
95P LEU* 4.7 1.2 - - + +
96P SER* 1.3 72.8 - - - +
98P SER* 1.3 58.2 + - - +
99P ASP* 2.9 33.9 + - - +
104P LYS* 3.6 9.5 - - - +
108P LEU* 3.1 13.9 - - - +
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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