Contacts of the strand formed by residues 642 - 650 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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780B LEU* 4.5 6.0 - - - +
593C VAL* 4.3 4.9 - - + -
594C VAL 3.5 7.2 - - - +
595C ARG* 3.1 27.6 - - - +
602C SER* 4.3 0.2 - - - -
638C ILE* 3.6 9.5 - - - +
639C ALA 3.0 32.1 + - - +
640C GLY 3.6 0.7 - - - +
641C ARG* 1.3 84.2 - - - +
643C LEU* 1.3 59.9 + - - +
644C TYR* 3.3 32.4 + - + -
734D ASN* 2.7 31.2 + - - +
738D VAL* 4.2 7.1 - - - +
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Residues in contact with LEU 643 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C PRO 3.8 1.0 - - - +
593C VAL* 3.5 2.1 - - - -
594C VAL* 2.9 52.9 + - + +
596C LEU* 4.7 3.6 - - + -
602C SER* 4.3 9.2 - - - +
605C VAL* 3.5 38.8 - - + -
606C LYS* 4.4 8.1 - - + +
609C LEU* 4.5 2.0 - - + -
636C THR* 4.1 17.0 - - - -
637C SER 3.7 7.0 - - - +
638C ILE* 3.5 23.1 - - + -
642C ASN* 1.3 76.0 - - - +
644C TYR* 1.3 71.3 + - - +
645C ILE* 3.9 17.7 + - + +
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Residues in contact with TYR 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C PRO 3.5 3.1 - - - -
593C VAL* 3.4 30.4 - - + +
635C HIS 3.9 0.7 - - - +
636C THR* 3.3 6.4 - - - -
637C SER* 2.8 45.6 + - - +
639C ALA* 3.9 16.6 - - + -
642C ASN* 3.3 27.0 + - + -
643C LEU* 1.3 74.8 - - - +
645C ILE* 1.3 61.2 + - - +
685C GLY 3.7 11.0 - - - -
687C TYR* 3.7 34.3 - + + -
734D ASN 2.7 25.9 + - - -
738D VAL* 3.0 20.3 - - + +
739D GLY* 3.5 15.5 - - - -
742D MET* 3.9 14.6 - - + -
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Residues in contact with ILE 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590C ARG 3.5 0.5 - - - +
591C GLY* 3.2 3.9 - - - -
592C PRO* 3.0 35.0 + - + +
594C VAL* 4.4 9.4 - - + -
609C LEU* 3.9 22.2 - - + -
634C LEU* 3.7 27.4 - - + -
635C HIS 3.8 2.2 - - - -
636C THR* 4.3 7.9 - - + -
643C LEU* 3.9 22.9 - - + +
644C TYR* 1.3 77.0 - - - +
646C ARG* 1.3 62.5 + - - +
647C PHE* 3.4 24.3 + - + -
668C LEU* 4.3 15.5 - - + -
671C LEU* 4.0 19.3 - - + -
687C TYR* 4.3 0.9 - - - -
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Residues in contact with ARG 646 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589C THR* 3.6 31.0 + - + +
590C ARG 3.6 4.5 - - - +
591C GLY* 4.3 1.8 - - - -
633C LYS* 3.6 3.0 - - - +
634C LEU* 3.3 9.3 - - - -
635C HIS* 2.8 46.3 + - + +
645C ILE* 1.3 70.6 - - - +
647C PHE* 1.3 64.1 + - - +
648C GLN* 3.8 9.6 + - + +
687C TYR* 3.6 22.0 + - + +
688C CYS 2.7 25.7 + - - -
696C ILE* 3.6 25.7 - - - +
697C ASN* 3.1 18.2 + - - +
700C GLU* 3.4 25.6 + - - +
701C GLY 2.9 29.5 + - - -
702C ARG* 3.9 1.8 - - - +
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Residues in contact with PHE 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588C MET 3.8 0.2 - - - +
589C THR* 3.0 26.7 - - - -
590C ARG 2.9 14.5 + - - +
592C PRO* 4.0 1.6 - - + -
609C LEU* 6.3 1.3 - - + -
618C ILE* 3.2 31.0 - - + -
622C PHE* 3.6 26.0 - + + -
631C LEU* 3.9 5.4 - - + -
633C LYS 4.0 2.9 - - - -
634C LEU* 3.6 11.0 - - + -
645C ILE* 3.4 38.1 - - + -
646C ARG* 1.3 72.7 - - - +
648C GLN* 1.3 59.4 + - - +
649C SER 4.3 0.2 - - - -
660C ILE* 4.3 3.2 - - + +
664C THR* 3.9 36.3 - - + +
667C ALA* 3.7 19.3 - - + -
668C LEU* 4.2 19.1 - - + -
671C LEU* 6.1 1.8 - - + -
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Residues in contact with GLN 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585C ALA* 5.9 4.6 - - - +
586C ASP 4.9 0.8 - - - +
587C GLY* 3.0 26.5 + - - +
588C MET 3.3 9.6 - - - +
589C THR* 3.7 15.4 - - + +
631C LEU* 3.4 5.6 - - - +
632C GLN* 2.8 46.5 + - - +
633C LYS* 3.2 40.3 + - + +
646C ARG* 4.7 8.5 + - + +
647C PHE* 1.3 75.6 - - - +
649C SER* 1.3 66.4 + - - +
700C GLU* 4.8 6.4 + - - +
701C GLY 4.5 13.5 + - - -
702C ARG* 4.8 0.4 - - - +
703C GLY 5.1 0.6 + - - -
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Residues in contact with SER 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587C GLY* 3.9 0.9 - - - -
588C MET* 2.9 34.5 + - - +
622C PHE* 3.7 26.5 - - - -
629C ALA* 3.8 3.3 - - - -
630C ARG 3.0 30.9 + - - -
631C LEU* 4.2 0.2 - - - -
632C GLN* 3.6 9.2 - - - +
648C GLN* 1.3 78.3 - - - +
650C ARG* 1.3 82.3 + - - +
660C ILE* 3.9 8.0 - - - +
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Residues in contact with ARG 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585C ALA* 5.8 1.6 - - - +
586C ASP* 3.2 45.1 + - - +
587C GLY* 4.6 1.3 - - - -
628C PHE 3.2 15.5 - - - +
630C ARG* 3.9 11.5 + - + +
632C GLN* 2.9 28.9 - - + +
649C SER* 1.3 92.8 + - - +
651C SER* 1.3 60.6 + - - +
652C GLY 4.7 2.7 - - - +
659C MET* 4.3 0.2 - - - +
660C ILE* 4.0 3.5 - - - +
836C ARG* 5.1 10.4 - - - +
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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