Contacts of the strand formed by residues 686 - 694 (chain A) in PDB entry 6DGD
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 TRP 686 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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640A ALA 4.0 0.3 - - - +
641A GLU* 3.1 22.1 - - - -
642A ASP* 2.9 29.1 + - - +
643A HIS 3.8 12.0 + - - -
644A ASN* 3.7 6.0 - - - +
645A ASN* 3.3 55.3 - - + +
680A PRO* 3.8 7.9 - - + +
681A LYS* 4.1 21.3 - - + -
684A GLY 3.4 19.0 + - - -
685A ARG* 1.3 72.9 - - - +
687A ARG* 1.3 63.0 + - - +
688A TRP* 4.0 7.9 + - - +
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Residues in contact with ARG 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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639A ARG* 6.4 1.3 - - + -
640A ALA 3.9 4.7 - - - +
641A GLU* 3.4 24.9 + - + +
676A PRO* 3.5 7.4 - - - +
677A ALA* 2.9 41.5 + - + +
679A ALA* 2.7 40.3 + - - +
680A PRO 3.0 13.8 + - - +
682A ARG* 4.0 29.4 - - - +
685A ARG 4.8 2.2 - - - +
686A TRP* 1.3 74.7 - - - +
688A TRP* 1.3 65.2 + - - +
805A SO4 3.6 32.5 + - - -
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Residues in contact with TRP 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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461A ARG* 4.6 16.4 - - - -
466A ASP* 4.4 7.0 - - - -
639A ARG* 3.4 3.1 - - - +
640A ALA 3.0 33.0 + - - +
642A ASP* 5.1 0.4 - - - -
645A ASN* 4.0 30.7 + - - +
648A ALA* 4.6 2.7 - - + -
649A PRO* 3.3 49.3 - - + +
652A LEU* 3.8 15.7 - - + -
674A PRO* 3.9 15.3 - - + -
675A VAL 3.4 26.7 - - - -
676A PRO* 3.4 32.0 - - + +
677A ALA* 5.0 0.8 - - - +
686A TRP* 4.3 13.2 - - + +
687A ARG* 1.3 81.4 - - - +
689A GLN* 1.3 65.9 + - - +
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Residues in contact with GLN 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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463A HIS* 3.4 28.8 + - + -
637A LEU* 4.1 22.5 - - + +
638A ILE 3.2 13.2 - - - +
639A ARG* 4.2 11.6 - - + +
652A LEU* 3.7 5.6 - - - -
673A GLY* 4.5 0.7 - - - -
674A PRO* 3.5 2.9 - - - +
675A VAL* 2.8 44.0 + - + +
676A PRO 4.5 0.7 - - - +
677A ALA* 3.7 27.3 - - + +
678A LEU* 4.8 1.3 + - - +
688A TRP* 1.3 78.6 - - - +
690A ILE* 1.3 63.3 + - - +
691A LEU* 5.9 3.8 - - - +
730A GLU* 4.0 17.5 + - - +
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Residues in contact with ILE 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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636A VAL 3.7 1.4 - - - +
637A LEU* 3.5 4.1 - - - +
638A ILE* 2.8 67.8 + - + +
652A LEU* 4.3 21.5 - - + +
655A LEU* 5.8 2.9 - - + -
656A ARG* 3.7 38.1 - - + +
659A LEU* 5.4 0.9 - - + -
671A VAL* 4.4 4.7 - - + +
672A LEU 3.2 22.0 - - - +
673A GLY* 3.8 14.8 - - - -
674A PRO* 4.1 2.7 - - + -
689A GLN* 1.3 75.2 - - - +
691A LEU* 1.3 60.1 + - - +
692A LEU* 4.1 13.4 - - + +
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Residues in contact with LEU 691 (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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464A HIS* 5.7 4.7 - - + -
629A LEU* 6.2 0.4 - - + -
635A HIS* 3.3 43.5 - - + +
636A VAL 3.5 1.8 - - - -
637A LEU* 3.1 33.7 - - + -
670A TRP 3.5 1.9 - - - +
671A VAL* 3.1 3.5 - - - -
672A LEU* 3.0 63.9 + - + +
689A GLN* 5.9 4.3 - - - +
690A ILE* 1.3 73.4 - - - +
692A LEU* 1.3 69.7 + - - +
693A GLN* 5.2 3.4 - - - +
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Residues in contact with LEU 692 (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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635A HIS* 3.3 4.2 - - - -
636A VAL* 2.8 49.9 + - + +
638A ILE* 4.2 11.2 - - + -
659A LEU* 3.4 24.7 - - + -
669A LEU* 4.3 5.6 - - + -
670A TRP 3.3 4.9 - - - -
671A VAL* 3.3 24.2 - - + -
690A ILE* 4.1 18.8 - - + +
691A LEU* 1.3 79.6 - - - +
693A GLN* 1.3 63.2 + - - +
700A LEU* 4.1 14.5 - - + +
703A ILE* 5.7 0.9 - - + -
704A VAL* 3.4 33.2 - - + -
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Residues in contact with GLN 693 (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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627A MET 5.2 1.4 + - - -
628A GLN* 3.4 25.6 + - - +
629A LEU* 4.9 4.6 - - - +
633A THR* 4.3 10.4 - - - +
634A SER 3.0 5.4 - - - +
635A HIS* 3.3 38.2 + - + +
668A LYS 3.6 6.2 - - - +
669A LEU* 3.3 4.8 - - - +
670A TRP* 2.9 56.9 + - + +
672A LEU* 4.8 12.3 - - + +
691A LEU* 5.1 1.9 - - + +
692A LEU* 1.3 75.5 - - - +
694A HIS* 1.3 66.2 + - - +
695A PRO* 5.8 0.9 - - - +
700A LEU* 3.9 3.1 - - - +
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Residues in contact with HIS 694 (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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633A THR* 4.4 4.0 - - - -
634A SER* 2.9 31.7 + - - +
666A ASP* 3.2 22.4 + - - -
668A LYS* 3.6 17.8 - - + +
669A LEU* 3.3 35.7 - - + -
693A GLN* 1.3 76.1 + - - +
695A PRO* 1.3 77.5 - - + +
696A SER* 3.0 34.7 + - - +
699A ARG* 3.5 25.8 - - + +
700A LEU* 3.8 25.3 - - + +
703A ILE* 4.5 4.3 - - + -
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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