Contacts of the strand formed by residues 413 - 418 (chain A) in PDB entry 5GSA
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 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A MET* 3.2 19.1 - - - +
367A ARG 5.3 0.9 - - - +
380A GLY* 3.7 16.0 + - - +
381A ASN 3.1 8.5 + - - +
384A GLY* 3.3 33.4 - - - +
385A LYS 3.4 19.5 - - - +
386A LEU* 4.1 14.8 - - + -
409A CYS* 4.3 5.8 - - - -
412A ALA* 1.4 67.3 - - - +
414A ARG* 1.3 63.0 + - - +
415A GLN 3.9 3.8 - - - +
416A THR* 3.8 19.5 - - + -
427A ALA* 3.8 22.7 - - + -
428A VAL 3.4 13.5 - - - +
429A CYS* 3.7 19.5 - - - -
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Residues in contact with ARG 414 (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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96A LEU 3.3 26.7 - - - +
97A PHE* 4.0 27.2 - - + +
363A ILE* 3.7 20.0 - - - +
364A TRP 3.2 18.8 + - - -
365A TYR 2.9 24.7 + - - +
366A MET* 3.7 14.4 - - - -
367A ARG* 3.1 29.7 + - - +
412A ALA* 4.2 6.5 - - - +
413A ILE* 1.3 73.1 - - - +
415A GLN* 1.3 62.0 + - - +
428A VAL 3.2 5.0 + - - +
430A ASP* 2.8 41.7 + - - +
501A 73K 3.6 32.8 + - - -
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Residues in contact with GLN 415 (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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97A PHE 4.1 9.0 - - - +
98A GLY* 3.2 9.6 - - - -
99A VAL* 3.1 41.8 + - + +
100A GLN* 3.5 17.6 + - - +
149A THR* 5.7 1.0 + - - -
150A CYS 6.0 0.2 + - - -
195A GLU* 4.8 2.2 + - - -
313A ARG* 4.2 11.9 - - - +
367A ARG* 3.5 43.4 + - + +
369A SER* 4.3 9.5 + - - +
413A ILE* 3.4 1.8 - - - +
414A ARG* 1.3 81.5 - - - +
416A THR* 1.3 81.0 + - - +
427A ALA* 3.7 1.6 - - - -
428A VAL* 3.1 28.2 + - + +
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Residues in contact with THR 416 (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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99A VAL* 3.6 4.8 - - - +
100A GLN* 5.9 0.2 - - - -
367A ARG 4.6 2.4 + - - +
369A SER* 2.8 35.2 + - - -
378A ALA* 3.8 16.0 + - + +
379A LEU* 4.7 1.3 - - - -
380A GLY 4.3 8.5 - - - +
386A LEU* 3.7 28.9 - - + -
413A ILE* 3.8 17.3 - - + -
415A GLN* 1.3 86.3 + - - +
417A SER* 1.3 63.6 + - - +
425A LEU* 4.0 11.5 - - - +
426A ILE 3.1 10.5 - - - -
427A ALA* 4.2 4.7 - - + -
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Residues in contact with SER 417 (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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99A VAL* 3.7 25.8 - - - -
100A GLN* 3.6 7.5 + - - -
101A PHE* 3.0 42.8 + - - +
103A TRP* 4.9 2.6 + - - -
369A SER* 4.9 2.9 - - - -
416A THR* 1.3 76.6 - - - +
418A PHE* 1.3 62.0 + - - +
425A LEU* 3.3 5.6 - - - -
426A ILE 2.8 38.4 + - - -
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Residues in contact with PHE 418 (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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82A PHE* 4.0 14.4 - + - -
101A PHE* 3.3 8.2 - - - +
103A TRP* 2.7 33.9 + - + -
369A SER* 4.4 4.9 - - - -
370A MET* 3.7 9.6 + - - +
371A ASP* 3.5 43.7 - - + -
376A MET* 3.6 39.9 - - + -
378A ALA* 3.8 30.1 - - + -
388A VAL* 4.7 4.7 - - + -
417A SER* 1.3 74.7 + - - +
419A SER* 1.3 58.9 + - - +
422A SER* 4.3 10.5 - - - -
424A ILE 3.3 11.2 - - - -
425A LEU* 3.8 23.6 - - + -
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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