Contacts of the strand formed by residues 319 - 324 (chain A) in PDB entry 4Q8E
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 ILE 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A PRO* 5.5 3.4 - - + -
318A THR* 1.3 80.4 - - - +
320A GLY* 1.3 56.7 + - - +
348A LEU* 3.4 22.6 - - + +
351A ARG* 3.7 37.7 - - + +
352A LEU* 4.0 15.3 - - + -
355A ASP* 3.7 40.4 - - + +
361A ARG* 4.5 5.4 - - - +
425A CYS* 4.1 1.3 - - - -
426A ALA 2.7 38.0 + - - +
429A PHE* 3.9 15.9 - - + -
7T C 3.9 3.1 - - - -
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A THR* 4.2 0.4 - - - -
319A ILE* 1.3 75.7 - - - +
321A CYS* 1.3 60.0 + - - -
348A LEU* 4.6 2.0 - - - -
351A ARG* 2.8 24.6 + - - -
423A PHE* 4.1 7.2 - - - -
424A LEU 3.3 9.2 - - - -
425A CYS* 3.9 11.6 - - - -
6T T 3.3 15.4 - - - +
7T C 3.1 12.4 + - - -
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Residues in contact with CYS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS* 3.6 6.5 - - - -
320A GLY* 1.3 74.4 - - - +
322A SER* 1.3 60.4 + - - +
344A LEU* 3.5 49.9 - - + +
347A GLU* 3.5 38.1 - - - -
348A LEU* 4.7 10.1 - - + +
351A ARG* 4.5 1.6 - - - +
423A PHE* 3.5 2.2 - - - -
424A LEU* 2.8 36.6 + - + +
6T T 3.7 3.6 - - - -
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Residues in contact with SER 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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86A LYS* 3.5 6.8 - - - -
321A CYS* 1.3 75.6 - - - +
323A LYS* 1.3 63.8 + - - +
324A ASN* 6.0 0.4 - - - -
344A LEU* 4.1 3.8 - - - -
421A MET* 5.1 5.2 - - - -
422A LEU 3.3 9.9 - - - -
423A PHE* 3.4 24.1 - - - -
5T C 3.3 32.4 + - - +
6T T 3.1 33.5 + - - +
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Residues in contact with LYS 323 (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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39A TYR* 3.2 27.7 + - - -
85A GLY 3.2 22.2 + - - +
86A LYS* 3.9 12.6 - - + -
322A SER* 1.3 77.2 - - - +
324A ASN* 1.3 75.7 + - - +
325A PHE* 3.4 28.0 - - + -
340A TRP* 3.7 32.1 - - + -
344A LEU* 4.3 12.7 - - + +
421A MET* 3.4 2.0 - - - -
422A LEU 3.0 33.3 + - - +
5T C 3.6 11.0 + - - +
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Residues in contact with ASN 324 (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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322A SER* 6.0 0.5 - - - -
323A LYS* 1.3 93.8 + - - +
325A PHE* 1.3 65.8 + - - +
326A PRO* 3.6 12.3 - - + +
420A THR 3.4 7.9 - - - +
421A MET* 3.4 23.2 - - - +
4T P9G 3.5 49.5 + - - +
5T C 2.9 18.9 + - - +
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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