Contacts of the strand formed by residues 357 - 361 (chain A) in PDB entry 2IAG
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 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A TYR* 5.7 0.2 - - + -
86A VAL* 6.0 0.7 - - + -
87A VAL* 4.2 19.1 - - + -
355A PRO* 4.0 3.8 + - + +
356A PHE* 1.3 74.0 - - - +
358A THR* 1.3 58.3 + - - +
359A ARG* 3.6 26.2 - - + +
383A LEU 3.6 0.9 - - - +
384A LEU* 3.4 4.0 - - - +
385A LEU* 2.7 57.9 + - + +
387A PRO* 3.5 31.9 - - + -
432A MET* 4.3 16.4 - - + -
435A GLY* 4.3 13.5 - - - -
436A ALA* 4.3 18.4 - - + +
439A ASN 6.0 0.9 - - - +
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Residues in contact with THR 358 (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 PHE* 4.0 11.1 - - - +
99A TYR* 4.1 29.7 - - + +
356A PHE* 3.4 15.9 + - - +
357A ILE* 1.3 74.5 - - - +
359A ARG* 1.3 82.2 + - - +
360A GLU* 4.3 4.5 - - - +
382A ARG* 3.7 34.2 - - + +
383A LEU 3.2 3.1 - - - -
384A LEU* 3.3 22.7 - - - +
439A ASN* 5.3 1.3 + - - +
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Residues in contact with ARG 359 (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 VAL* 4.7 11.8 + - + -
87A VAL* 3.3 30.7 + - - +
89A GLU 5.5 2.2 + - - -
94A LEU* 4.0 35.9 + - + +
95A ASP 3.5 3.6 - - - -
96A PHE* 3.8 38.3 - - - +
357A ILE* 3.6 23.6 - - + +
358A THR* 1.3 90.7 + - - +
360A GLU* 1.3 65.0 + - - +
382A ARG* 3.3 4.5 - - - +
383A LEU* 2.6 53.9 + - + +
385A LEU* 6.5 0.4 - - + -
436A ALA 3.8 16.8 + - - -
438A HIS 4.5 2.6 - - - +
439A ASN* 4.1 18.6 - - - +
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Residues in contact with GLU 360 (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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72A ARG* 2.6 38.7 + - - -
94A LEU* 3.5 3.1 - - - -
95A ASP* 2.7 48.0 + - + +
98A ALA* 4.1 23.1 - - + -
99A TYR* 4.4 9.5 - - + +
358A THR* 4.3 5.2 - - - +
359A ARG* 1.3 73.1 - - - +
361A VAL* 1.3 61.3 + - - +
362A VAL* 3.2 11.1 + - + +
380A GLY* 6.4 0.4 - - - -
381A ASP 3.8 1.3 - - - +
382A ARG* 2.9 32.6 + - - +
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Residues in contact with VAL 361 (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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75A THR* 6.2 0.4 - - - -
93A ARG 4.0 2.9 - - - -
94A LEU* 4.1 14.6 - - + -
360A GLU* 1.3 70.2 - - - +
362A VAL* 1.3 58.4 - - - +
363A VAL 3.7 19.3 - - - +
365A LEU* 4.1 6.1 - - + -
377A LEU* 3.9 29.8 - - + +
378A ARG 3.5 27.6 - - - +
379A ARG* 3.4 1.1 - - - +
380A GLY* 2.8 29.8 + - - -
381A ASP* 2.8 36.0 + - + +
383A LEU* 4.4 11.2 - - + -
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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