Contacts of the strand formed by residues 580 - 585 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A MET* 2.9 40.0 + - + +
29A TRP 3.2 11.0 - - - +
30A VAL* 3.6 17.3 - - - +
31A PRO* 5.0 0.4 - - - -
179A PHE* 3.9 9.5 - - - -
269A VAL* 3.7 0.9 - - - +
270A ALA* 3.3 5.0 - - - +
271A GLY 2.7 34.4 + - - +
273A PRO* 3.6 29.3 - - + +
573A PRO* 3.0 25.2 + - - +
574A ASP 2.8 24.9 + - - -
575A ALA* 3.7 5.8 - - - +
576A ASN* 3.1 23.6 + - - -
578A SER* 3.3 16.8 + - - +
579A LEU* 1.4 88.5 - - - +
581A ILE* 1.3 65.8 + - - +
582A THR* 5.7 0.6 - - - +
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Residues in contact with ILE 581 (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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27A GLY 3.7 0.7 - - - +
28A MET* 4.9 0.2 - - - -
29A TRP* 2.9 41.0 + - + +
30A VAL 5.5 0.4 - - - -
31A PRO* 5.2 10.5 - - + -
34A LEU* 5.1 14.4 - - + -
37A ILE* 4.5 20.4 - - + -
41A LEU* 5.0 7.9 - - + -
53A ILE* 4.8 8.7 - - + -
56A LEU* 6.4 0.2 - - + -
61A MET* 3.4 37.5 - - + -
268A MET* 5.0 9.6 - - + -
269A VAL 3.3 4.0 - - - +
270A ALA* 3.6 17.3 - - + -
579A LEU* 5.5 0.7 - - + -
580A ARG* 1.3 77.9 - - - +
582A THR* 1.3 74.6 + - - +
583A PHE* 4.6 4.3 - - + -
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Residues in contact with THR 582 (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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25A GLY 3.9 3.8 + - - -
27A GLY 3.6 13.0 + - - -
28A MET* 5.1 0.7 - - - -
29A TRP* 4.7 0.2 - - - -
268A MET* 3.3 4.5 - - - +
269A VAL* 2.8 52.1 + - + +
580A ARG 5.7 0.4 - - - +
581A ILE* 1.3 74.1 - - - +
583A PHE* 1.3 66.8 + - - +
650A LEU* 3.6 9.2 - - + -
651A ASP* 2.9 47.0 + - - +
652A ILE* 3.9 11.9 - - + -
656A ASN* 5.7 0.7 - - - +
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Residues in contact with PHE 583 (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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25A GLY 2.8 31.9 + - - +
26A GLU 6.0 0.7 - - - -
29A TRP* 3.8 24.9 - + - -
37A ILE* 3.9 27.8 - - + -
40A PRO* 3.7 41.5 - - + -
41A LEU* 3.2 32.5 - - + -
44A ALA* 4.2 15.0 - - + -
266A PHE* 4.0 2.9 - - + -
267A VAL 3.4 11.4 - - - +
268A MET* 4.0 5.4 - - + -
581A ILE* 4.6 1.3 - - + -
582A THR* 1.3 83.5 + - - +
584A GLY* 1.3 55.2 + - - +
650A LEU* 3.5 7.9 - - - +
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Residues in contact with GLY 584 (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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25A GLY 3.9 4.0 - - - -
44A ALA* 4.8 1.8 - - - -
266A PHE* 3.5 8.2 - - - -
267A VAL 3.0 26.3 + - - +
583A PHE* 1.3 81.1 - - - +
585A ASN* 1.3 77.2 + - - -
649A ASP* 3.2 12.8 - - - -
650A LEU* 3.4 4.2 - - - +
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Residues in contact with ASN 585 (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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44A ALA* 2.9 36.5 + - - +
264A GLY* 3.1 25.2 - - - +
265A ASP 3.2 5.2 - - - -
266A PHE 3.6 5.2 + - - -
267A VAL* 4.2 1.8 - - - -
584A GLY* 1.3 93.5 + - - +
586A VAL* 1.3 64.8 + - - +
587A MET* 3.3 20.5 + - + +
648A SER* 3.2 5.6 - - - -
649A ASP* 2.8 31.6 + - - +
650A LEU* 4.0 1.4 - - - +
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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