Contacts of the helix formed by residues 642 - 654 (chain D) in PDB entry 1S77
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 LYS 642 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637D LEU 5.7 0.2 + - - -
640D GLY* 3.2 21.4 + - - +
641D SER* 1.3 75.2 - - - +
643D GLU* 1.3 59.1 + - - +
644D PHE* 3.1 7.2 - - + +
645D GLY* 2.6 25.1 + - - +
646D PHE* 3.1 13.4 + - - -
682D TRP* 3.3 26.2 - - + -
696D MET* 4.9 9.7 - - - +
697D ASN* 5.6 4.0 - - - +
700D LYS* 3.9 18.8 - - - +
120T T 3.5 5.3 + - - -
121T A 5.0 1.8 + - - +
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Residues in contact with GLU 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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642D LYS* 1.3 73.4 - - - +
644D PHE* 1.3 62.5 + - - +
646D PHE* 3.2 18.6 + - - +
647D ARG* 3.2 9.9 + - - +
675D GLY 4.7 2.6 - - - +
678D ALA* 3.6 24.2 - - + +
679D LYS* 3.5 37.1 + - - +
682D TRP* 3.2 41.6 + - + -
683D GLU* 5.6 0.2 - - - +
21N T 5.4 0.7 - - - +
22N G 4.3 14.3 + - - -
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Residues in contact with PHE 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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642D LYS* 3.1 6.0 - - + +
643D GLU* 1.3 75.8 - - - +
645D GLY* 1.3 67.9 + - - +
647D ARG* 3.0 57.2 + - + +
648D GLN* 3.6 7.9 + - + +
20N T 3.4 24.2 - + - -
21N T 4.1 22.9 - + - +
121T A 3.0 66.9 - + + +
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Residues in contact with GLY 645 (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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641D SER* 4.2 0.9 - - - -
642D LYS* 2.6 19.0 + - - +
644D PHE* 1.3 74.4 - - - +
646D PHE* 1.3 62.2 + - - -
648D GLN* 2.9 18.7 + - - +
649D GLN* 3.0 19.7 + - - +
120T T 3.5 26.9 + - - -
121T A 4.5 7.4 + - - +
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Residues in contact with PHE 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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633D SER* 3.4 45.3 + - - +
637D LEU* 4.2 9.6 - - + -
641D SER* 3.7 37.2 - - - -
642D LYS 3.4 5.2 - - - -
643D GLU* 3.3 12.3 - - - +
645D GLY* 1.3 74.6 - - - +
647D ARG* 1.3 55.9 + - - +
649D GLN* 3.0 12.7 + - - +
650D VAL* 2.6 37.0 + - - +
678D ALA* 3.6 29.8 - - + -
681D ILE* 3.8 12.1 - - + -
682D TRP* 3.7 32.1 - + - -
685D VAL* 3.9 8.5 - - + -
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Residues in contact with ARG 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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643D GLU 3.2 6.1 + - - +
644D PHE* 3.0 36.0 - - + +
645D GLY 3.1 0.6 + - - -
646D PHE* 1.3 77.3 - - - +
648D GLN* 1.3 59.4 + - - +
650D VAL* 3.0 6.2 - - - +
651D LEU* 2.9 45.9 + - + +
671D ASN* 2.6 36.1 - - - +
674D ALA* 4.1 5.6 - - + +
675D GLY* 4.0 24.8 - - - +
678D ALA* 3.4 17.5 - - + +
20N T 2.6 58.0 + - - +
21N T 5.6 3.4 - - - -
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Residues in contact with GLN 648 (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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644D PHE* 3.6 8.2 + - + +
645D GLY* 2.9 11.4 + - - +
647D ARG* 1.3 80.5 - - - +
649D GLN* 1.3 58.3 + - + +
651D LEU* 4.1 16.6 - - + +
652D GLU* 2.8 58.4 + - - +
653D ASP* 5.6 0.2 - - - +
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Residues in contact with GLN 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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632D ARG* 3.5 29.9 + - + +
633D SER* 2.6 51.3 + - - +
636D THR* 3.2 7.0 + - - -
641D SER* 2.9 24.9 + - - -
645D GLY 3.1 10.7 - - - +
646D PHE* 3.0 13.3 + - - +
648D GLN* 1.3 76.9 - - + +
650D VAL* 1.3 60.2 + - - +
653D ASP* 2.6 47.0 + - - +
120T T 3.5 15.2 - - + +
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Residues in contact with VAL 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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620D TRP* 3.5 25.6 - - + -
629D VAL* 4.1 14.6 - - + +
633D SER* 5.3 1.2 + - - -
646D PHE 2.6 17.3 + - - +
647D ARG* 3.0 14.4 - - - +
649D GLN* 1.3 72.5 - - - +
651D LEU* 1.3 74.8 + - - +
653D ASP* 4.8 1.1 - - - -
654D THR* 2.9 43.3 + - - +
655D ILE* 3.0 4.8 + - + -
674D ALA* 3.5 29.2 - - + +
677D MET* 3.6 18.2 - - + -
678D ALA 4.6 1.8 - - - +
681D ILE* 5.1 4.9 - - + -
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Residues in contact with LEU 651 (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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647D ARG* 2.9 36.5 + - - +
648D GLN* 3.4 19.3 - - + +
650D VAL* 1.3 86.1 - - - +
652D GLU* 1.3 59.7 + - + +
655D ILE* 3.3 8.5 - - + +
656D GLN* 2.5 41.6 + - + +
670D PRO* 3.3 44.9 - - + -
671D ASN* 4.5 5.8 - - - +
674D ALA* 4.0 7.9 - - + -
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Residues in contact with GLU 652 (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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386D ARG* 3.6 19.4 + - - -
648D GLN* 2.8 42.1 + - - +
649D GLN 4.3 0.4 - - - +
651D LEU* 1.3 78.6 - - - +
653D ASP* 1.3 63.0 + - - +
656D GLN* 3.0 37.5 + - - +
657D PRO* 3.0 21.7 - - - +
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Residues in contact with ASP 653 (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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628D SER 6.1 0.2 - - - +
632D ARG* 2.7 53.6 + - + +
648D GLN* 5.6 0.3 - - - +
649D GLN* 2.6 28.5 + - - +
650D VAL* 4.8 0.4 - - - -
652D GLU* 1.3 78.9 - - - +
654D THR* 1.3 67.5 + - + +
657D PRO* 3.4 10.4 - - - +
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Residues in contact with THR 654 (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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620D TRP* 4.2 2.4 - - - -
623D TYR* 3.7 16.2 + - - -
628D SER* 4.3 7.9 - - - +
629D VAL* 3.8 39.9 - - + +
650D VAL* 2.9 30.7 + - - +
653D ASP* 1.3 88.3 - - + +
655D ILE* 1.3 64.6 + - - +
657D PRO* 3.5 5.2 - - - +
658D ALA* 2.9 28.9 + - - +
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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