Contacts of the strand formed by residues 685 - 690 (chain A) in PDB entry 4FOV
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 VAL 685 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.7 15.1 - - - +
232A ILE 5.2 0.5 + - - -
233A PHE* 4.4 12.5 + - + +
244A PHE* 3.3 38.6 - - + +
245A ARG* 4.4 2.5 - - - -
247A PRO* 4.2 7.2 - - + -
261A ILE* 3.7 24.2 - - + -
667A LEU* 4.0 23.0 - - + +
668A PHE 3.2 9.4 - - - +
669A GLU* 4.0 22.0 - - + -
671A TYR* 5.3 0.4 - - + -
683A ASN* 4.5 1.3 - - - +
684A VAL* 1.3 80.2 + - + +
686A GLN* 1.3 63.8 + - - +
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Residues in contact with GLN 686 (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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131A ALA 6.0 0.4 + - - -
134A TRP* 2.8 32.6 + - - +
164A ILE* 4.0 5.1 - - - +
229A PHE* 3.3 37.6 - - + -
230A GLN 3.9 3.6 - - - -
231A LEU* 4.1 4.9 - - + +
667A LEU* 3.3 6.4 - - - -
668A PHE* 2.8 48.8 + - + +
670A LYS* 3.6 11.6 - - - +
683A ASN 3.1 19.6 + - - -
684A VAL* 3.5 15.9 - - - +
685A VAL* 1.3 81.4 - - - +
687A TYR* 1.3 60.6 + - - +
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Residues in contact with TYR 687 (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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229A PHE* 3.4 5.4 - - - -
230A GLN* 2.9 61.8 + - + +
232A ILE* 3.9 23.1 - - + -
249A LEU* 4.1 9.4 - - + -
285A ASN 4.1 0.3 + - - -
286A GLY* 3.7 24.7 - - - -
289A TRP* 3.9 16.3 - + - -
659A LEU* 3.4 35.2 - - + +
665A GLY* 3.6 17.3 - - - -
666A VAL 3.1 17.0 - - - -
667A LEU* 3.7 15.5 - - + +
686A GLN* 1.3 74.0 - - - +
688A ILE* 1.3 77.7 + - - +
689A ASP* 4.5 6.3 + - + -
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Residues in contact with ILE 688 (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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134A TRP* 3.7 27.4 - - + -
137A HIS* 4.1 17.7 - - + +
228A PRO 3.4 24.0 - - - +
229A PHE* 4.0 2.5 - - + +
230A GLN* 5.8 0.4 - - - -
642A TYR* 5.4 0.4 - - + -
644A ILE* 3.9 34.8 - - + +
664A ILE 3.9 0.3 - - - +
665A GLY* 3.7 0.7 - - - -
666A VAL* 2.8 48.4 + - + +
668A PHE* 4.0 13.5 - - + -
687A TYR* 1.3 88.6 - - - +
689A ASP* 1.3 59.8 + - - +
690A LEU* 4.1 14.8 - - + -
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Residues in contact with ASP 689 (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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137A HIS* 4.2 4.4 + - - -
138A LYS* 3.5 21.3 + - - -
228A PRO 5.3 1.0 + - - -
230A GLN* 5.5 3.6 + - - +
285A ASN 4.1 6.8 - - - +
659A LEU* 3.3 26.0 - - - +
661A ASN* 5.2 0.9 + - - -
663A HIS* 2.9 31.8 + - - -
664A ILE 3.5 3.6 - - - -
665A GLY* 4.9 0.2 - - - -
687A TYR* 4.5 10.0 + - + -
688A ILE* 1.3 74.8 - - - +
690A LEU* 1.3 69.5 + - - +
691A GLU* 4.7 1.6 - - - +
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Residues in contact with LEU 690 (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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137A HIS* 4.0 8.1 - - + -
138A LYS* 3.9 19.7 - - + +
624A LEU* 3.7 29.2 - - + -
642A TYR* 3.6 39.9 - - + +
644A ILE* 4.4 0.9 - - + -
663A HIS* 3.2 7.3 - - - +
664A ILE* 2.6 44.3 + - + +
666A VAL* 4.2 7.9 - - + -
688A ILE* 4.1 18.6 - - + -
689A ASP* 1.3 83.0 + - - +
691A GLU* 1.3 67.3 + - - +
694A ASP* 3.8 7.9 - - + +
695A LEU* 4.0 7.0 - - + -
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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