Contacts of the strand formed by residues 361 - 365 (chain C) in PDB entry 1EQB
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 GLY 361 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C VAL 3.1 13.5 - - - -
323C LEU* 4.1 6.7 - - - -
330C GLY* 3.2 16.6 - - - +
347C ASN 2.8 31.2 + - - -
349C VAL* 4.0 5.8 - - - -
359C THR 3.5 1.2 - - - -
360C SER* 1.3 81.4 - - - +
362C ILE* 1.3 66.2 + - - +
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Residues in contact with ILE 362 (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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302C PHE* 5.0 1.3 - - + -
319C PHE 4.1 0.3 - - - +
320C LEU* 3.6 2.7 - - - +
321C VAL* 2.9 50.5 + - + +
323C LEU* 4.1 2.7 - - + -
330C GLY 4.1 8.3 - - - +
333C ALA* 3.6 28.3 - - + -
334C ASP 4.4 3.4 - - - +
337C LEU* 4.0 24.2 - - + -
344C VAL* 4.6 11.2 - - + -
345C ASN 3.6 11.2 - - - +
346C LYS* 4.6 0.9 - - - -
347C ASN* 4.0 4.3 - - - +
349C VAL* 5.2 0.4 - - - +
361C GLY* 1.3 81.2 - - - +
363C ARG* 1.3 59.8 + - - +
364C VAL* 4.3 16.6 - - + -
386C MET* 4.4 6.3 - - + -
390C LEU* 4.7 13.7 - - + -
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Residues in contact with ARG 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU 3.7 8.5 - - - +
33C ILE* 4.2 0.8 - - - +
34C ALA* 3.8 22.4 - - + +
35C SER* 3.5 15.2 + - - +
175C SER 2.8 30.3 + - - -
176C ALA* 4.0 9.6 - - + -
203C HIS* 3.6 2.8 + - - -
318C LEU* 4.2 7.4 - - + -
319C PHE 3.7 6.3 - - - +
320C LEU* 3.7 14.8 - - + -
344C VAL* 4.0 13.0 - - - +
345C ASN* 3.2 37.7 + - - +
347C ASN* 3.6 23.6 + - + +
362C ILE* 1.3 71.3 - - - +
364C VAL* 1.3 70.6 + - - +
3292C GLY* 2.8 39.4 + - - -
3293C FFO 3.8 12.0 + - - -
65D PHE* 3.9 4.8 - - - -
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Residues in contact with VAL 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.5 31.4 - - + -
34C ALA* 4.4 2.5 - - - -
298C MET* 4.4 10.1 - - + -
302C PHE* 5.1 1.3 - - + -
317C HIS 3.9 0.2 - - - +
318C LEU* 3.1 8.7 - - - +
319C PHE* 2.9 71.1 + - + +
321C VAL* 4.8 1.1 - - + -
344C VAL* 4.7 2.7 - - + -
362C ILE* 4.3 23.1 - - + +
363C ARG* 1.3 81.9 - - - +
365C GLY* 1.3 62.5 + - - +
386C MET* 4.3 12.8 - - + -
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Residues in contact with GLY 365 (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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31C GLU 4.4 1.9 - - - +
32C LEU* 2.9 40.2 + - - +
33C ILE 5.0 0.4 - - - -
34C ALA* 3.8 22.6 - - - +
317C HIS 3.4 9.2 - - - -
364C VAL* 1.3 75.8 - - - +
366C THR* 1.3 62.7 + - - -
367C PRO* 3.3 5.8 - - - -
368C ALA* 5.1 0.9 + - - +
369C ILE* 5.0 0.2 - - - +
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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