Contacts of the strand formed by residues 642 - 650 (chain A) in PDB entry 1DQ8
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 ASN 642 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A VAL* 4.3 5.3 - - + +
594A VAL 3.4 6.7 - - - +
595A ARG* 3.1 27.7 - - - +
602A SER* 4.5 0.2 - - - -
638A ILE* 3.6 5.7 - - - +
639A ALA 3.0 35.3 + - - +
640A GLY 3.7 3.1 - - - +
641A ARG* 1.3 83.5 - - - +
643A LEU* 1.3 61.8 + - - +
644A TYR* 3.2 33.1 + - + -
734B ASN* 2.8 32.7 + - - +
738B VAL* 4.4 4.8 - - - +
780D LEU* 4.8 5.4 - - - +
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Residues in contact with LEU 643 (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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592A PRO 3.9 0.7 - - - +
593A VAL* 3.7 1.0 - - - -
594A VAL* 2.9 47.4 + - + +
596A LEU* 4.8 2.0 - - + -
602A SER* 3.9 15.9 - - - +
605A VAL* 3.5 38.8 - - + -
606A LYS* 4.2 8.1 - - + +
609A LEU* 4.3 2.5 - - + -
636A THR* 3.9 18.4 - - + -
637A SER 3.6 12.3 - - - +
638A ILE* 4.1 13.7 - - + -
642A ASN* 1.3 76.4 - - - +
644A TYR* 1.3 73.3 + - - +
645A ILE* 3.8 20.0 + - + +
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Residues in contact with TYR 644 (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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592A PRO 3.6 3.1 - - - -
593A VAL* 3.4 30.6 - - + +
635A HIS 3.9 0.5 - - - +
636A THR* 3.3 8.1 - - - -
637A SER* 2.7 45.6 + - - +
639A ALA* 4.0 8.1 - - + -
642A ASN* 3.2 29.0 + - + -
643A LEU* 1.3 74.3 - - - +
645A ILE* 1.3 61.8 + - - +
685A GLY 3.6 11.2 - - - -
687A TYR* 3.7 35.6 - + + -
734B ASN 2.6 25.5 + - - -
738B VAL* 3.2 15.7 - - + +
739B GLY* 3.6 17.9 - - - -
742B MET* 3.9 21.3 - - + -
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Residues in contact with ILE 645 (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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590A ARG 3.4 0.3 - - - +
591A GLY* 3.2 4.0 - - - -
592A PRO* 2.9 42.8 + - + +
594A VAL* 4.6 11.2 - - + -
609A LEU* 4.0 20.6 - - + -
634A LEU* 4.0 24.2 - - + -
635A HIS 3.8 1.6 - - - -
636A THR* 4.1 9.2 - - + -
643A LEU* 3.8 25.1 - - + +
644A TYR* 1.3 77.2 - - - +
646A ARG* 1.3 61.4 + - - +
647A PHE* 3.5 25.2 + - + -
668A LEU* 4.1 14.8 - - + -
671A LEU* 4.0 20.2 - - + -
687A TYR* 4.4 0.9 - - - -
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Residues in contact with ARG 646 (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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589A THR* 3.8 30.4 + - + +
590A ARG 3.6 4.0 - - - +
591A GLY* 4.2 2.2 - - - -
633A LYS 3.8 1.2 - - - +
634A LEU* 3.5 7.3 - - - -
635A HIS* 2.9 48.3 + - + +
644A TYR 4.1 0.4 - - - -
645A ILE* 1.3 72.2 - - - +
647A PHE* 1.3 65.2 + - - +
648A GLN* 4.6 10.1 + - + +
687A TYR* 3.6 23.5 + - + +
688A CYS 2.8 25.7 + - - +
696A ILE* 3.9 19.8 + - - +
697A ASN* 3.2 21.4 + - - +
700A GLU* 3.3 25.9 + - - +
701A GLY 3.0 27.7 + - - -
702A ARG* 4.0 2.6 - - - +
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Residues in contact with PHE 647 (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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588A MET 3.7 0.2 - - - +
589A THR* 3.1 26.9 - - - -
590A ARG 2.9 14.1 + - - +
592A PRO* 3.7 17.9 - - + -
609A LEU* 6.1 1.3 - - + -
618A ILE* 3.9 15.7 - - + -
622A PHE* 3.7 26.2 - + + -
631A LEU* 3.9 4.7 - - + -
633A LYS 4.1 3.6 - - - -
634A LEU* 3.8 14.6 - - + -
645A ILE* 3.5 34.1 - - + -
646A ARG* 1.3 72.4 - - - +
648A GLN* 1.3 59.2 + - - +
660A ILE* 4.6 2.9 - - + +
664A THR* 3.7 27.1 - - + +
667A ALA* 3.6 27.8 - - + -
668A LEU* 4.0 17.9 - - + -
671A LEU* 5.9 1.3 - - + -
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Residues in contact with GLN 648 (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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585A ALA* 5.9 4.2 - - - +
586A ASP 4.9 1.0 - - - +
587A GLY* 3.1 28.5 + - - +
588A MET 3.2 10.8 - - - +
589A THR* 3.7 14.1 - - + +
631A LEU* 3.6 5.1 - - - +
632A GLN* 2.8 43.5 + - - +
633A LYS* 3.3 23.0 + - - +
646A ARG* 4.6 10.6 + - + +
647A PHE* 1.3 75.8 - - - +
649A SER* 1.3 66.1 + - - +
700A GLU* 4.7 7.1 + - - +
701A GLY 4.3 15.2 + - - -
702A ARG* 4.7 0.2 - - - +
703A GLY 5.1 0.8 + - - -
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Residues in contact with SER 649 (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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588A MET* 2.9 30.9 + - - +
622A PHE* 3.8 14.3 - - - -
629A ALA* 3.9 1.9 - - - -
630A ARG 3.3 28.8 + - - -
631A LEU* 3.8 0.7 - - - -
632A GLN* 3.3 11.2 - - - +
648A GLN* 1.3 78.8 - - - +
650A ARG* 1.3 84.1 + - - +
660A ILE* 3.2 22.9 - - - +
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Residues in contact with ARG 650 (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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585A ALA* 5.7 1.4 - - - +
586A ASP* 2.9 56.0 + - - +
587A GLY* 4.7 1.3 - - - -
628A PHE 3.2 18.2 - - - +
629A ALA* 4.2 0.7 - - - -
630A ARG* 3.8 19.8 + - + +
632A GLN* 3.0 24.4 + - + +
649A SER* 1.3 91.5 + - - +
651A SER* 1.3 60.1 + - - +
652A GLY 4.6 3.4 - - - +
659A MET* 4.3 1.2 - - - +
660A ILE* 4.5 0.2 - - - +
836A ARG* 4.4 17.6 - - - +
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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