Contacts of the strand formed by residues 92 - 96 (chain D) in PDB entry 1C7G
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 HIS 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D LYS* 4.4 3.9 + - - +
90D PHE* 4.2 3.1 - - - +
91D LYS* 1.3 94.2 + - + +
93D ILE* 1.3 63.3 + - - +
268D CYS* 3.4 8.3 - - - +
269D MET* 2.9 43.3 + - - +
270D ASN 3.8 8.5 - - - -
271D ASP 4.3 0.4 - - - -
272D GLU* 2.5 38.3 + - + +
275D PHE* 3.4 60.3 - + + -
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Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D PHE* 4.5 10.9 - - + -
80D LEU* 3.9 23.6 - - + -
81D GLU* 3.6 43.4 + - + +
84D VAL* 3.7 33.4 - - + -
85D LYS* 4.5 3.6 - - + +
92D HIS* 1.3 79.1 - - - +
94D VAL* 1.3 70.8 + - - +
95D PRO* 3.9 8.8 - - + +
266D PHE* 4.0 26.7 - - + -
267D LEU 3.3 7.2 - - - +
268D CYS* 4.2 5.8 - - - -
275D PHE* 4.3 7.7 - - - -
289D PRO 5.2 0.2 - - - +
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 1.3 78.8 - - - +
95D PRO* 1.3 76.8 - - + +
96D THR* 4.1 1.4 - - - +
105D LEU* 4.8 8.1 - - + -
266D PHE* 3.4 2.2 - - - -
267D LEU* 2.7 48.5 + - + +
269D MET* 4.6 4.9 - - - -
275D PHE* 3.8 27.6 - - + -
278D ALA* 4.3 20.4 - - + +
279D LYS* 5.2 2.5 - - + +
282D VAL* 4.1 29.8 - - + -
289D PRO* 4.7 8.5 - - + -
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Residues in contact with PRO 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D PHE* 3.8 26.2 - - + -
80D LEU* 4.4 14.6 - - + -
93D ILE* 3.9 3.8 - - + +
94D VAL* 1.3 93.7 - - + +
96D THR* 1.3 63.4 + - - +
265D GLY 3.7 10.8 - - - +
266D PHE* 3.8 3.3 - - + -
282D VAL* 4.1 1.9 - - - +
289D PRO 3.2 26.2 - - - +
291D TYR* 3.8 22.4 - - - +
292D GLY* 3.4 17.2 - - - -
294D LEU* 4.4 9.9 - - + -
299D MET* 4.5 2.5 - - - -
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Residues in contact with THR 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D VAL 4.1 7.4 - - - +
95D PRO* 1.3 79.7 - - - +
97D HIS* 1.3 65.3 + - - +
98D GLN 2.8 23.8 + - - -
102D ALA* 3.7 17.6 - - + +
105D LEU* 3.8 28.7 - - + -
265D GLY 2.9 31.9 + - - +
266D PHE* 3.4 4.7 + - - -
267D LEU* 5.0 0.7 - - + +
282D VAL* 4.7 0.2 - - + -
286D GLU* 3.5 16.8 - - + -
292D GLY 3.2 9.9 - - - -
294D LEU* 3.5 7.3 - - - +
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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