Contacts of the strand formed by residues 361 - 364 (chain A) in PDB entry 2W2M
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 LEU 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A ILE* 3.8 28.0 - - + -
335A THR 3.4 0.2 + - - -
336A VAL* 3.3 20.2 - - + -
337A GLY 2.9 21.8 + - - -
359A VAL* 3.4 4.8 - - - +
360A ASP* 1.3 83.0 - - + +
362A PHE* 1.3 72.9 + - - +
392A VAL* 4.2 10.1 - - + -
415A LEU* 4.4 23.3 - - + +
416A ILE* 5.3 2.7 - - + +
419A SER* 3.6 20.6 - - - +
438A PRO* 4.5 1.8 - - - -
440A LEU* 4.0 20.9 - - + +
442A ALA* 3.7 20.4 - - + -
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Residues in contact with PHE 362 (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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336A VAL* 4.1 1.6 - - - -
337A GLY* 3.1 31.9 - - - +
338A ALA 3.7 9.4 - - - -
339A THR* 3.7 21.8 - - + +
345A PRO* 5.1 2.0 - - + -
353A THR* 4.1 13.2 - - + -
354A ASN 4.1 16.4 - - - -
355A PHE* 4.9 0.4 - - - -
359A VAL* 4.1 13.5 - - + -
361A LEU* 1.3 77.9 - - - +
363A ALA* 1.3 57.8 + - - +
424A ILE* 3.6 20.0 - - + -
429A PHE* 3.9 15.5 - + - -
437A THR* 3.6 25.4 - - + -
438A PRO* 3.4 23.3 - - + -
440A LEU 2.8 13.7 + - - +
441A VAL* 3.3 3.0 - - + -
442A ALA* 2.8 33.3 + - - +
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Residues in contact with ALA 363 (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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336A VAL* 3.8 7.9 - - + -
337A GLY 2.9 10.8 + - - +
338A ALA* 3.4 1.7 - - - -
339A THR* 3.0 22.9 + - - -
362A PHE* 1.3 76.7 - - - +
364A PRO* 1.4 77.8 - - + +
365A GLY 3.3 0.3 + - - -
388A ALA* 3.4 26.1 - - - +
391A HIS* 4.1 5.6 - - + -
392A VAL* 3.9 11.7 - - + -
441A VAL* 4.4 2.0 - - - -
442A ALA* 4.0 6.5 - - + +
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Residues in contact with PRO 364 (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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156A TRP* 3.6 19.7 - - + -
157A ASN* 3.5 44.2 - - + +
160A ARG* 4.3 7.9 - - + -
161A ILE* 3.9 21.1 - - + -
339A THR* 3.5 10.3 - - - +
363A ALA* 1.4 84.5 - - + -
365A GLY* 1.3 58.5 + - - +
368A ILE* 3.9 3.1 - - + -
388A ALA* 3.3 10.0 + - - -
391A HIS* 3.2 26.8 + - + +
441A VAL* 4.5 9.6 - - + -
442A ALA 4.9 0.2 - - - +
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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