Contacts of the strand formed by residues 642 - 650 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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780A LEU* 4.9 4.4 - - - +
734C ASN* 2.8 32.8 + - - +
738C VAL* 4.4 5.5 - - - +
593D VAL* 4.4 4.9 - - + +
594D VAL 3.5 7.0 - - - +
595D ARG* 3.3 25.1 - - - +
602D SER* 4.6 0.2 - - - -
638D ILE* 3.7 6.4 - - - +
639D ALA 3.0 32.2 + - - +
640D GLY 3.7 2.9 - - - +
641D ARG* 1.3 85.0 - - - +
643D LEU* 1.3 60.3 + - - +
644D TYR* 3.1 34.5 + - + +
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Residues in contact with LEU 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592D PRO 3.9 0.7 - - - +
593D VAL* 3.6 2.6 - - - -
594D VAL* 2.9 46.3 + - + +
596D LEU* 4.9 1.3 - - + -
602D SER* 4.3 8.7 - - - +
605D VAL* 3.5 39.0 - - + -
606D LYS* 4.3 5.6 - - + +
609D LEU* 4.3 4.9 - - + -
636D THR* 4.1 17.7 - - - -
637D SER 3.7 8.5 - - - +
638D ILE* 3.6 24.5 - - + -
642D ASN* 1.3 76.3 - - - +
644D TYR* 1.3 71.3 + - - +
645D ILE* 3.8 23.7 + - + +
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Residues in contact with TYR 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734C ASN 2.6 30.0 + - - -
738C VAL* 3.2 12.3 - - + +
739C GLY* 3.6 16.2 - - - -
742C MET* 3.9 16.2 - - + -
592D PRO 3.5 3.8 - - - -
593D VAL* 3.4 27.5 - - + +
635D HIS 3.8 0.7 - - - +
636D THR* 3.3 5.7 - - - -
637D SER* 2.8 43.2 + - - +
639D ALA* 3.8 15.9 - - + -
642D ASN* 3.1 33.7 + - + -
643D LEU* 1.3 73.7 - - - +
645D ILE* 1.3 61.1 + - - +
646D ARG 4.1 0.2 - - - -
685D GLY 3.8 10.8 - - - -
687D TYR* 3.7 33.2 - + + -
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Residues in contact with ILE 645 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591D GLY* 3.3 2.9 - - - -
592D PRO* 2.9 37.8 + - + +
594D VAL* 4.4 11.9 - - + -
609D LEU* 4.0 11.4 - - + -
634D LEU* 3.9 22.4 - - + -
635D HIS 3.7 2.0 - - - +
636D THR* 4.3 9.6 - - + +
643D LEU* 3.8 31.6 - - + +
644D TYR* 1.3 77.0 - - - +
646D ARG* 1.3 59.8 + - - +
647D PHE* 3.4 27.3 - - + -
668D LEU* 4.4 14.1 - - + -
671D LEU* 4.0 24.7 - - + -
687D TYR* 4.4 0.6 - - - -
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Residues in contact with ARG 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589D THR* 3.7 29.1 + - + +
590D ARG 3.6 4.7 - - - +
591D GLY* 4.1 2.2 - - - -
633D LYS 3.8 0.3 - - - +
634D LEU* 3.4 6.8 - - - -
635D HIS* 2.7 47.5 + - + +
644D TYR 4.1 0.6 - - - -
645D ILE* 1.3 70.0 - - - +
647D PHE* 1.3 65.6 + - - +
648D GLN* 3.8 12.4 + - + +
687D TYR* 3.6 21.2 + - + +
688D CYS* 2.8 27.6 + - - +
696D ILE* 3.7 24.9 - - - +
697D ASN* 3.2 20.4 + - - +
700D GLU* 3.4 24.8 - - - +
701D GLY 2.9 29.1 + - - -
702D ARG* 3.9 2.6 - - - +
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Residues in contact with PHE 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588D MET 3.8 0.2 - - - +
589D THR* 3.1 27.1 - - - -
590D ARG* 2.9 15.2 + - + +
592D PRO* 3.9 4.5 - - + -
609D LEU* 6.2 1.6 - - + -
618D ILE* 3.2 29.4 - - + -
622D PHE* 3.7 26.9 - + + -
631D LEU* 4.1 2.0 - - + -
634D LEU* 3.7 15.9 - - + -
645D ILE* 3.4 40.4 - - + -
646D ARG* 1.3 73.2 - - - +
648D GLN* 1.3 59.5 + - - +
649D SER 4.2 0.2 - - - -
660D ILE* 4.7 2.4 - - + +
664D THR* 3.7 35.0 - - + +
667D ALA* 3.5 21.3 - - + -
668D LEU* 4.1 16.4 - - + -
671D LEU* 6.1 1.6 - - + -
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Residues in contact with GLN 648 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585D ALA* 5.9 3.8 - - - +
586D ASP 4.8 1.4 - - - +
587D GLY* 2.9 38.8 + - - +
588D MET 3.4 3.1 - - - +
589D THR* 3.8 14.0 - - + +
631D LEU* 3.3 5.3 - - - +
632D GLN* 2.8 33.0 + - - +
633D LYS* 3.1 46.8 + - + +
646D ARG* 4.4 9.7 + - + +
647D PHE* 1.3 74.6 - - - +
649D SER* 1.3 64.4 + - - +
700D GLU* 4.8 8.2 + - - +
701D GLY 4.4 14.5 + - - -
702D ARG* 4.8 0.2 - - - +
703D GLY 5.0 0.6 + - - -
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Residues in contact with SER 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587D GLY* 4.0 5.6 - - - -
588D MET* 2.9 36.2 + - - +
622D PHE* 3.5 32.1 - - - -
629D ALA 3.9 0.3 - - - -
630D ARG 3.1 24.9 + - - -
631D LEU* 3.7 2.2 - - - -
632D GLN* 4.0 3.4 - - - +
647D PHE 4.2 0.2 - - - -
648D GLN* 1.3 77.6 - - - +
650D ARG* 1.3 83.1 + - - +
651D SER* 4.6 0.2 + - - -
660D ILE* 3.6 8.4 - - - +
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Residues in contact with ARG 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586D ASP* 3.1 53.9 + - - +
587D GLY* 4.7 1.1 - - - -
628D PHE 3.3 14.1 - - - +
629D ALA* 3.9 2.3 - - - -
630D ARG* 3.3 15.6 + - + +
632D GLN* 3.4 25.7 + - + +
649D SER* 1.3 91.4 + - - +
651D SER* 1.3 60.6 + - - +
652D GLY 4.8 2.7 - - - +
660D ILE* 4.1 1.4 - - - +
831D PRO 5.3 0.4 + - - -
836D ARG* 4.0 23.7 - - - +
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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