Contacts of the strand formed by residues 663 - 672 (chain B) in PDB entry 4DQL
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 PHE 663 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B GLY 3.6 14.6 - - - +
662B ALA* 1.3 74.2 - - - +
664B SER* 1.3 61.9 + - - +
665B THR* 4.0 16.4 - - + -
689B LEU* 4.0 16.4 - - + -
690B PRO* 3.6 31.0 - - + -
693B ALA* 3.8 28.3 - - + -
878B ILE 3.7 0.5 - - - +
879B THR* 3.3 7.2 - - - -
880B CYS* 3.0 55.7 + - - +
881B PHE* 4.0 9.6 - - - -
882B ILE* 4.3 14.4 - - + -
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Residues in contact with SER 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B PHE* 1.3 76.9 - - - +
665B THR* 1.3 59.0 + - - +
690B PRO* 5.9 1.2 - - - +
877B THR* 3.1 25.9 - - - +
878B ILE 3.4 4.5 - - - -
879B THR* 4.0 12.1 + - - -
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Residues in contact with THR 665 (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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663B PHE* 4.0 11.9 - - + -
664B SER* 1.3 75.3 - - - +
666B ASN* 1.3 69.5 + - - +
687B ILE* 3.5 20.2 - - + -
688B GLU* 2.5 38.7 + - - +
689B LEU 4.8 0.2 - - - -
690B PRO* 4.6 5.7 - - - +
877B THR* 3.1 7.3 - - - +
878B ILE* 2.8 41.7 + - + +
880B CYS* 3.8 15.0 - - - -
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Residues in contact with ASN 666 (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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665B THR* 1.3 85.9 + - - +
667B VAL* 1.3 66.2 + - - +
668B VAL* 3.5 3.2 + - + -
687B ILE* 3.8 3.7 - - - +
688B GLU* 3.0 44.0 + - + +
875B GLY* 4.1 11.5 - - - +
876B ASP 3.4 7.2 - - - +
877B THR* 3.0 24.3 + - - -
878B ILE* 4.8 0.2 - - - -
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Residues in contact with VAL 667 (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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666B ASN* 1.3 72.9 - - - +
668B VAL* 1.3 57.0 + - - +
669B ALA 3.4 28.9 - - - +
670B SER* 4.3 5.8 - - - -
685B LEU* 4.5 7.4 - - + -
686B GLU 3.7 7.0 - - - +
687B ILE* 4.3 6.3 - - + -
872B LEU* 3.9 31.9 - - + -
873B GLN 3.7 21.8 - - - +
874B GLU* 3.5 0.9 - - - -
875B GLY* 2.9 28.2 + - - -
876B ASP* 2.9 21.3 + - + +
878B ILE* 4.3 14.6 - - + -
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Residues in contact with VAL 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B ASN* 3.5 3.1 + - + +
667B VAL* 1.3 72.7 - - - +
669B ALA* 1.3 61.9 + - + +
686B GLU* 2.8 20.2 + - + +
688B GLU* 4.1 30.5 - - + +
842B GLN* 3.8 31.4 - - - +
874B GLU* 3.9 13.6 - - - +
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Residues in contact with ALA 669 (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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667B VAL* 3.4 10.0 - - - +
668B VAL* 1.3 82.2 - - + +
670B SER* 1.3 63.3 + - - +
671B LYS* 6.0 0.2 - - + -
684B HIS* 4.2 1.6 - - + -
685B LEU* 3.2 5.6 - - - -
686B GLU* 2.9 45.7 + - + -
874B GLU* 5.0 4.5 - - - -
1104B PG4 3.9 25.4 - - - -
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Residues in contact with SER 670 (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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667B VAL* 4.3 7.6 - - - -
669B ALA* 1.3 76.9 - - - +
671B LYS* 1.3 64.8 + - - +
683B ARG* 3.3 19.4 + - - -
684B HIS 3.3 7.2 - - - -
685B LEU* 4.3 12.3 - - - +
869B LEU 4.6 1.9 + - - -
872B LEU 2.9 30.9 + - - -
873B GLN* 4.5 5.6 - - - -
874B GLU* 4.7 2.8 - - - +
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Residues in contact with LYS 671 (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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669B ALA* 6.0 0.2 - - + -
670B SER* 1.3 78.3 + - - +
672B GLU* 1.4 63.4 + - - +
673B LEU* 4.6 0.4 - - - -
683B ARG* 3.4 18.1 + - - +
684B HIS* 2.8 48.7 + - + +
1104B PG4 2.7 109.9 + - - +
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Residues in contact with GLU 672 (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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671B LYS* 1.4 76.2 - - - +
673B LEU* 1.3 60.4 - - - +
674B GLN* 2.8 43.6 + - + +
680B ARG 4.8 0.9 - - - -
681B SER* 2.5 31.8 + - - -
682B THR 3.0 21.1 + - - +
683B ARG* 3.4 18.7 + - - +
1104B PG4 4.0 18.0 - - - -
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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