Contacts of the strand formed by residues 668 - 675 (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 LEU 668 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A SER* 5.1 0.7 - - - +
75A VAL* 4.3 21.3 - - + -
82A VAL* 4.7 8.5 - - + -
254A LEU* 4.1 12.3 - - + +
255A LYS 2.8 21.8 + - - +
256A PHE* 3.8 39.0 - - + +
257A ALA* 3.0 21.5 + - - +
660A PRO* 3.6 27.1 - - + -
661A VAL 3.5 5.2 - - - +
662A LEU* 4.2 3.2 - - - +
666A GLY 4.2 0.2 + - - -
667A LYS* 1.3 68.6 - - - +
669A VAL* 1.3 58.1 + - - +
670A GLY* 3.3 28.9 - - - +
671A LEU* 4.5 6.3 - - + -
698A GLY* 5.2 0.7 - - - -
701A LEU* 5.5 3.8 - - + -
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Residues in contact with VAL 669 (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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257A ALA* 3.5 26.9 - - + -
259A GLN 4.8 2.0 - - - +
261A LEU* 4.0 23.1 - - + -
267A VAL* 4.1 11.2 - - + -
646A TYR* 2.9 27.6 + - - +
661A VAL* 2.8 28.9 + - + +
662A LEU 4.0 0.7 - - - -
663A ASP* 3.7 30.3 - - + +
668A LEU* 1.3 71.7 - - - +
670A GLY* 1.3 57.9 + - - +
697A ASP* 3.7 5.7 - - - +
698A GLY* 3.1 18.9 + - - +
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Residues in contact with GLY 670 (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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646A TYR* 3.7 7.4 + - - -
661A VAL* 2.8 26.8 + - - -
668A LEU* 3.3 16.9 - - - +
669A VAL* 1.3 81.5 - - - +
671A LEU* 1.3 66.0 + - - +
696A VAL 2.9 14.6 - - - -
698A GLY* 3.6 8.0 - - - +
701A LEU* 5.8 0.7 - - - -
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Residues in contact with LEU 671 (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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82A VAL* 3.9 30.7 - - + +
83A THR 3.2 32.8 - - - +
84A ASN* 3.7 13.5 - - - +
224A ASP 3.9 1.8 - - - +
225A PHE* 3.7 21.1 - - + -
658A GLY 4.2 13.9 - - - +
659A SER 3.4 6.1 - - - +
660A PRO* 4.4 6.3 - - + -
661A VAL* 3.9 0.4 - - - +
668A LEU* 4.5 7.2 - - + -
670A GLY* 1.3 84.1 - - - +
672A ALA* 1.3 63.6 + - - +
673A PHE 3.5 0.2 + - - -
695A ALA* 3.1 6.2 - - - -
696A VAL* 2.9 40.3 + - + +
701A LEU* 4.5 8.1 - - + -
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Residues in contact with ALA 672 (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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84A ASN* 3.1 6.9 - - - +
269A VAL* 4.7 2.5 - - + -
652A ILE* 4.0 11.0 - - + -
656A ASN* 3.7 17.9 - - + +
657A SER* 4.4 1.3 - - - -
658A GLY 2.9 24.9 + - - -
659A SER* 3.0 19.4 + - - +
661A VAL* 3.7 4.1 - - + +
671A LEU* 1.3 70.7 - - - +
673A PHE* 1.3 58.6 + - - +
693A MET* 3.5 27.8 - - - -
694A ILE 4.0 5.2 - - - -
695A ALA* 4.2 0.4 - - - -
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Residues in contact with PHE 673 (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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84A ASN* 3.1 26.9 - - - +
220A ARG* 3.7 31.4 - - + -
222A THR* 3.8 17.5 - - + -
224A ASP* 3.4 22.9 - - + +
645A ASN* 3.3 31.4 - - - -
657A SER* 3.2 7.8 + - - +
671A LEU 3.9 1.3 - - - -
672A ALA* 1.3 71.8 - - - +
674A ASP* 1.3 66.1 + - + +
694A ILE* 2.9 27.6 + - + -
695A ALA 3.5 7.9 - - - -
696A VAL* 3.5 36.8 - - + -
1C VAL* 3.3 7.0 - - + +
2C TYR* 3.0 21.8 + - - -
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Residues in contact with ASP 674 (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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215A ASN* 3.3 0.9 - - - +
216A TRP* 2.8 36.2 + - - -
220A ARG* 2.8 37.3 + - - +
652A ILE* 3.8 1.6 - - - +
673A PHE* 1.3 85.3 - - + +
675A GLY* 1.3 62.3 + - - +
693A MET* 3.7 3.8 - - - -
694A ILE* 2.8 34.9 + - + +
1C VAL* 2.7 28.3 + - - -
2C TYR* 3.3 19.3 - - - -
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Residues in contact with GLY 675 (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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216A TRP* 3.5 26.8 - - - -
674A ASP* 1.3 81.7 + - - +
676A ASN* 1.3 67.9 + - - +
679A SER* 3.6 7.2 - - - -
692A ARG 3.6 10.1 - - - -
694A ILE* 3.7 6.1 - - - +
2C TYR* 3.1 19.5 - - - -
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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