Contacts of the strand formed by residues 2 - 7 (chain A) in PDB entry 5I2S
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 PHE 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A LYS* 1.3 78.6 - - - +
3A THR* 1.3 66.6 + - - +
4A ILE* 3.7 24.0 - - + -
334A ASP* 3.3 4.7 - - - -
335A ILE* 2.9 54.2 + - + +
336A ALA 4.4 2.7 - - - -
337A ALA* 3.7 24.0 - - - -
338A PRO* 3.7 28.0 - - + -
385A TYR* 3.9 26.2 - + + -
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Residues in contact with THR 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 1.3 77.2 - - - +
4A ILE* 1.3 69.9 + - - +
30A LEU* 4.0 35.4 - - + +
332A ARG* 3.5 32.8 - - + -
334A ASP* 2.7 28.2 + - - +
348A SER* 3.6 6.3 + - - +
385A TYR* 4.8 4.2 + - - -
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Residues in contact with ILE 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 3.7 22.9 - - + -
3A THR* 1.3 79.5 - - - +
5A VAL* 1.3 74.3 + - - +
6A PHE* 4.4 5.8 - - + -
332A ARG* 3.5 9.8 - - - +
333A VAL* 2.9 46.4 + - + +
335A ILE* 3.6 29.4 - - + -
356A LEU* 5.8 0.2 - - + -
382A PHE* 4.0 22.0 - - + -
385A TYR* 3.4 38.1 - - + +
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Residues in contact with VAL 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 1.3 88.5 - - - +
6A PHE* 1.3 68.6 + - - +
29A ASP* 5.9 0.9 - - - +
307A PRO 3.5 15.6 - - - +
308A LYS* 3.4 32.3 - - - +
309A ASN 3.6 4.9 - - - +
310A PRO* 3.9 27.8 - - + -
330A TYR* 4.1 15.2 - - + -
331A ILE 3.1 13.7 - - - +
332A ARG* 4.0 11.7 - - + +
333A VAL 4.6 0.2 - - - +
385A TYR* 4.7 4.8 + - - +
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Residues in contact with PHE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.4 4.5 - - + -
5A VAL* 1.3 79.8 - - - +
7A PRO* 1.3 106.0 - - + +
330A TYR* 3.6 6.4 - - - -
331A ILE* 2.9 30.5 + - + +
333A VAL* 4.0 18.6 - - + -
343A MET* 3.5 19.1 - - + -
356A LEU* 3.6 35.9 - - + -
357A TRP* 3.9 16.8 - + + -
370A PRO* 4.1 17.0 - - + -
371A ASN* 6.0 1.1 - - - -
373A VAL* 3.8 14.1 - - + -
382A PHE* 3.7 31.6 - + - -
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Residues in contact with PRO 7 (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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6A PHE* 1.3 116.0 - - + +
8A HIS* 1.3 63.9 + - - +
9A ASN* 3.4 6.0 - - + +
315A ALA* 4.5 2.7 - - + -
326A PHE* 5.5 0.4 - - + -
328A THR* 3.9 20.6 - - + +
329A ARG 3.4 8.5 - - - +
330A TYR* 3.4 29.6 - - + +
331A ILE* 4.8 0.9 - - - +
354A ARG* 4.0 6.6 + - - -
356A LEU 4.2 0.2 - - - +
357A TRP* 4.0 19.5 - - + -
370A PRO* 4.2 18.4 - - + -
371A ASN* 4.4 4.9 - - - +
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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