Contacts of the strand formed by residues 580 - 585 (chain B) in PDB entry 3WOO
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 ARG 580 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B MET* 3.1 36.5 + - + +
29B TRP 3.2 6.5 - - - +
30B VAL* 3.5 20.6 - - - +
31B PRO* 5.1 0.2 - - - -
179B PHE* 3.8 9.3 - - - -
269B VAL* 3.7 1.7 - - - +
270B ALA* 3.3 4.9 - - - +
271B GLY 2.8 31.7 + - - +
273B PRO* 3.6 25.2 - - + +
573B PRO* 2.7 29.7 + - - +
574B ASP 2.8 23.4 + - - -
575B ALA* 3.7 8.1 - - - +
576B ASN* 2.8 25.3 + - - +
578B SER* 3.3 21.8 + - - +
579B LEU* 1.3 83.2 - - - +
581B ILE* 1.3 65.5 + - - +
582B THR* 5.7 0.4 - - - +
656B ASN* 5.5 0.2 - - - +
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Residues in contact with ILE 581 (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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27B GLY 3.6 1.2 - - - +
28B MET* 4.8 0.7 - - - -
29B TRP* 2.9 46.0 + - + +
30B VAL 5.5 0.4 - - - +
31B PRO* 4.5 16.8 - - + -
34B LEU* 4.1 31.4 - - + -
37B ILE* 4.7 12.6 - - + -
41B LEU* 5.3 3.6 - - + -
53B ILE* 4.3 10.8 - - + -
61B MET* 3.7 32.8 - - + -
268B MET* 5.0 13.7 - - + -
269B VAL 3.3 8.7 - - - +
270B ALA* 4.5 2.5 - - + -
579B LEU* 5.6 0.7 - - + -
580B ARG* 1.3 77.9 - - - +
582B THR* 1.3 69.8 + - - +
583B PHE* 5.0 3.6 - - + -
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Residues in contact with THR 582 (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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25B GLY 4.1 3.1 + - - -
27B GLY 3.6 17.9 + - - -
28B MET* 5.1 0.9 - - - -
268B MET* 3.2 4.7 - - - +
269B VAL* 2.8 57.0 + - + +
580B ARG 5.7 0.4 - - - +
581B ILE* 1.3 75.6 - - - +
583B PHE* 1.3 68.2 + - - +
650B LEU* 3.6 9.3 - - + -
651B ASP* 2.8 41.1 + - - +
652B ILE* 3.8 13.7 - - + -
656B ASN* 5.6 0.7 - - - +
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Residues in contact with PHE 583 (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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25B GLY 2.9 26.2 + - - +
26B GLU 5.7 0.9 - - - -
29B TRP* 3.7 34.1 - + - -
37B ILE* 3.8 20.9 - - + -
40B PRO* 3.7 42.0 - - + -
41B LEU* 3.3 35.4 - - + -
44B ALA* 4.2 11.9 - - + -
266B PHE* 4.0 4.5 - + + -
267B VAL 3.4 11.2 - - - +
268B MET* 4.0 3.8 - - + -
581B ILE* 5.0 2.0 - - + -
582B THR* 1.3 81.4 + - - +
584B GLY* 1.3 60.0 + - - +
650B LEU* 3.5 8.7 - - - +
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Residues in contact with GLY 584 (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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25B GLY 4.0 3.6 - - - -
44B ALA* 4.7 2.2 - - - -
266B PHE* 3.5 8.2 - - - -
267B VAL 2.9 27.8 + - - +
583B PHE* 1.3 82.2 - - - +
585B ASN* 1.3 76.9 + - - -
649B ASP* 3.3 11.2 - - - -
650B LEU* 3.3 4.5 - - - +
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Residues in contact with ASN 585 (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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44B ALA* 3.1 33.8 - - - +
264B GLY* 3.1 24.4 - - - +
265B ASP 3.2 11.1 - - - +
267B VAL* 4.1 2.2 - - - -
584B GLY* 1.3 84.1 + - - +
586B VAL* 1.3 65.1 + - - +
587B MET* 3.4 20.1 + - + +
648B SER* 3.4 5.6 - - - -
649B ASP* 2.8 33.0 + - - +
650B LEU* 4.1 1.0 - - - +
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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