Contacts of the strand formed by residues 316 - 322 (chain A) in PDB entry 4IE6
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 ARG 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ASN* 4.0 1.9 - - - +
206A PHE* 3.5 3.2 - - - -
207A MET* 3.0 33.0 + - - +
244A VAL* 4.5 1.6 - - - +
246A SER* 2.6 33.3 + - - -
247A TYR 3.0 24.7 - - - +
248A SER* 3.6 11.4 - - - +
249A CYS* 4.5 2.7 - - - +
270A TRP* 3.6 40.7 - - + +
289A LEU* 3.7 15.2 - - - +
309A VAL* 3.6 20.2 - - - +
315A PRO* 1.3 78.0 - - - +
317A PHE* 1.3 65.5 + - - +
318A SER* 3.7 13.2 + - - +
602A UN9 3.0 40.0 + - - -
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Residues in contact with PHE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.7 46.2 - + + -
70A LEU* 3.9 24.0 - - + -
73A HIS* 3.8 30.5 - + + -
78A LEU* 4.2 9.4 - - + -
204A LEU* 6.3 0.2 - - + -
205A ASN 3.1 8.5 - - - +
206A PHE* 3.4 48.9 - + + -
247A TYR* 2.8 52.0 + + + +
249A CYS* 4.4 9.9 - - - -
316A ARG* 1.3 79.8 - - - +
318A SER* 1.3 62.4 + - - +
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.9 6.6 - - - -
204A LEU* 3.2 6.2 - - - +
205A ASN* 2.9 47.0 + - - +
244A VAL* 4.1 4.9 - - - -
245A TYR 3.3 11.9 - - - -
316A ARG* 3.7 18.6 + - - -
317A PHE* 1.3 75.8 - - - +
319A SER* 1.3 60.4 + - - +
320A THR* 3.8 0.9 - - - +
602A UN9 2.6 33.9 + - - -
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.9 16.4 - - - -
139A PHE* 3.6 14.2 - - - -
142A LEU* 4.1 8.3 - - - -
202A THR* 2.8 20.3 + - - -
203A LEU 4.0 1.8 - - - -
204A LEU* 3.6 9.0 - - - +
243A ALA 3.3 1.2 - - - +
245A TYR* 3.0 30.6 + - - -
318A SER* 1.3 72.0 - - - +
320A THR* 1.3 61.0 + - - +
321A HIS* 2.9 26.7 + - - -
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A THR* 3.3 5.0 + - - -
203A LEU* 3.0 35.2 + - - +
205A ASN* 3.6 20.9 + - - +
242A VAL* 4.8 2.9 - - - -
243A ALA 3.5 5.6 - - - -
244A VAL* 3.6 17.9 - - + -
318A SER* 3.8 5.6 - - - +
319A SER* 1.3 70.5 - - - +
321A HIS* 1.3 60.3 + - - +
322A ARG* 2.9 37.5 + - - -
602A UN9 3.6 26.2 - - - +
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Residues in contact with HIS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TRP* 4.7 0.2 - + - -
139A PHE* 3.7 14.1 - - + -
142A LEU* 3.6 9.4 - - + +
143A ASN* 2.6 44.6 + - - +
146A LEU* 3.3 22.2 - - + +
199A TYR* 3.7 24.0 - + + -
201A VAL 3.4 5.6 - - - -
202A THR* 3.6 13.9 - - + +
242A VAL* 3.4 9.0 - - - +
243A ALA* 2.9 34.9 + - + +
319A SER* 2.9 36.3 + - - -
320A THR* 1.3 71.2 - - - +
322A ARG* 1.3 61.2 + - - +
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 2.8 34.7 + - + -
199A TYR* 3.3 10.9 - - - -
200A ASN* 3.0 27.2 + - - +
201A VAL* 3.0 23.8 + - + +
203A LEU* 4.2 16.1 - - - +
233A ASP* 3.4 21.5 + - - +
236A LEU* 3.8 20.8 - - + +
241A ALA 4.5 3.1 - - - -
242A VAL* 4.2 11.2 - - + -
320A THR* 2.9 37.8 + - - -
321A HIS* 1.3 79.0 - - - +
323A VAL* 1.3 59.1 + - - +
324A ALA* 3.5 0.9 - - - +
602A UN9 2.7 47.8 + - - +
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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