Contacts of the strand formed by residues 356 - 360 (chain B) in PDB entry 4AY1
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 GLY 356 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B TYR* 4.2 6.5 - - - -
28B LYS 3.2 14.4 - - - -
262B VAL 3.8 2.8 + - - +
263B VAL* 3.7 6.2 - - - +
264B MET* 3.0 19.8 + - - +
349B LEU* 3.7 25.9 - - - +
354B LEU* 3.3 3.9 - - - +
355B GLY* 1.3 79.5 - - - +
357B ALA* 1.3 60.6 + - - -
387B LEU* 5.0 0.9 - - - -
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Residues in contact with ALA 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS 3.1 4.8 + - - -
29B LEU* 3.4 10.0 - - + +
30B VAL 3.0 21.7 + - - -
263B VAL* 3.4 9.0 - - - +
264B MET 3.3 9.0 - - - +
266B ILE* 3.9 10.5 - - + -
349B LEU* 3.8 18.6 - - + +
356B GLY* 1.3 73.8 - - - -
358B MET* 1.3 60.3 + - - +
359B ILE* 5.1 0.2 - - + -
383B VAL* 3.9 27.1 - - + -
387B LEU* 4.6 3.7 - - + +
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Residues in contact with MET 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.2 12.3 - - + +
32B TYR* 3.6 27.1 - - + -
208B ASN* 3.8 22.2 - - + +
209B LEU 3.3 28.0 - - - +
210B LEU* 3.8 23.8 - - + -
212B PHE* 4.1 6.1 - - + -
263B VAL* 3.8 18.2 - - + +
264B MET 2.8 7.5 + - - +
265B GLY* 3.5 9.6 - - - -
266B ILE* 2.6 36.2 + - - +
357B ALA* 1.3 74.6 - - - +
359B ILE* 1.3 75.4 + - - +
360B TRP* 3.8 4.5 - - - -
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Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.8 24.0 - - + -
30B VAL 2.8 12.8 + - - +
31B CYS* 4.1 7.4 - - - -
32B TYR* 3.2 28.6 + - - +
266B ILE* 3.4 16.8 - - + +
268B THR* 3.8 28.5 - - + -
342B MET* 5.3 2.0 - - - -
357B ALA* 5.1 0.2 - - + -
358B MET* 1.3 85.4 - - - +
360B TRP* 1.3 60.9 + - - +
361B SER* 3.8 5.9 - - - -
362B ILE* 3.9 22.9 - - + -
380B VAL* 3.9 14.4 - - + -
383B VAL* 4.2 27.6 - - + -
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Residues in contact with TRP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 3.4 48.7 - + + -
34B THR* 4.0 7.9 - - + -
36B TRP* 3.9 22.0 - + - -
62B SER* 3.6 12.8 - - - -
63B PHE* 3.6 31.6 - + - -
210B LEU* 5.6 3.8 - - + -
212B PHE* 3.4 32.3 - + + -
266B ILE 3.1 8.3 + - - -
267B PRO* 3.3 5.9 - - - +
268B THR* 3.0 24.1 + - - -
269B TYR* 3.6 22.8 - + - -
358B MET* 3.8 4.6 - - - -
359B ILE* 1.3 72.5 - - - +
361B SER* 1.3 56.3 + - - +
364B MET* 3.8 14.3 - - + +
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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