Contacts of the helix formed by residues 641 - 652 (chain A) in PDB entry 1SIW
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 HIS 641 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612A TYR* 3.2 26.9 - - - -
618A TRP* 2.9 34.6 + + + +
621A GLU* 3.3 19.9 - - + +
624A THR* 6.6 0.2 - - - +
640A GLY* 1.3 73.8 - - - -
642A LEU* 1.3 75.6 + - - +
643A ILE* 2.9 19.7 + - + +
644A ASP* 2.8 23.4 + - - +
645A PHE* 3.1 13.3 - - - -
743A LEU* 3.8 21.0 - - + +
749A VAL 4.9 4.7 - - - +
750A LYS 5.3 0.2 - - - -
751A PRO* 3.5 32.3 - - + +
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Residues in contact with LEU 642 (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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548A TYR* 4.8 0.2 - - - +
612A TYR* 4.0 4.3 - - - +
621A GLU* 4.0 7.4 - - - -
623A VAL* 3.7 30.4 + - + +
624A THR* 4.5 1.3 - - - +
625A ALA* 4.0 24.6 - - + +
628A LEU* 4.9 2.2 - - + -
640A GLY 4.0 0.6 + - - -
641A HIS* 1.3 82.9 + - + +
643A ILE* 1.3 59.9 + - - +
645A PHE* 3.2 21.6 + - + +
646A ASN 3.5 3.6 + - - -
1191A THR* 4.0 18.4 - - + -
1192A PRO* 3.4 34.1 - - + +
1194A PRO* 3.8 34.1 - - + -
1197A MET* 3.8 9.8 - - + +
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Residues in contact with ILE 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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612A TYR* 4.0 18.8 - - + -
613A ASN* 4.3 20.6 - - + +
618A TRP* 3.5 45.5 - - + +
641A HIS* 2.9 30.3 + - + +
642A LEU* 1.3 77.5 - - - +
644A ASP* 1.3 71.3 + - - +
646A ASN* 3.1 11.3 + - + +
647A VAL* 3.1 30.1 + - + +
696A ALA 5.8 1.1 - - - +
751A PRO* 4.1 7.4 - - + -
754A VAL* 4.3 14.4 - - + -
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Residues in contact with ASP 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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640A GLY 4.4 0.7 - - - -
641A HIS 2.8 31.8 + - - +
643A ILE* 1.3 81.5 - - - +
645A PHE* 1.3 61.2 + - - +
647A VAL* 3.4 2.8 + - - +
648A ARG* 3.1 40.6 + - - +
751A PRO* 3.1 21.6 - - - +
752A GLU* 2.7 31.9 + - - +
753A GLU* 3.1 33.1 + - + +
754A VAL* 3.9 1.9 + - - +
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Residues in contact with PHE 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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625A ALA* 3.5 26.9 - - + -
638A TYR* 3.7 37.2 - + + -
639A THR 4.0 9.4 - - - -
640A GLY 3.7 11.0 - - - -
641A HIS 3.1 19.3 - - - -
642A LEU* 3.2 12.5 + - + +
644A ASP* 1.3 77.4 - - - +
646A ASN* 1.3 58.4 + - - +
648A ARG* 3.5 16.6 + - - +
649A ALA* 3.0 27.7 + - - +
1050A TRP* 3.9 30.5 - + + -
1054A PHE* 3.9 22.9 - + - -
1194A PRO* 4.4 6.7 - - + -
1197A MET* 3.7 16.1 - - + +
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Residues in contact with ASN 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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605A MET* 5.8 0.2 - - - +
609A SER* 2.8 36.8 + - - -
612A TYR* 5.9 4.4 - - + -
642A LEU 3.5 2.8 + - - +
643A ILE* 3.1 19.1 + - + +
645A PHE* 1.3 80.5 - - - +
647A VAL* 1.3 57.4 + - + +
649A ALA* 3.0 4.6 + - - +
650A GLU* 2.8 62.7 + - - +
655A LEU* 3.7 17.0 - - - +
656A PRO 5.2 1.2 + - - -
1192A PRO* 5.5 1.0 - - - +
1197A MET* 3.6 24.1 - - + +
1213A THR* 4.3 1.2 - - - +
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Residues in contact with VAL 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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643A ILE* 3.1 19.0 + - + +
644A ASP 3.4 6.5 + - - +
646A ASN* 1.3 77.0 - - - +
648A ARG* 1.3 61.4 + - - +
650A GLU* 3.4 12.7 + - - +
651A ARG* 3.1 35.6 + - + +
694A PHE* 5.8 3.0 - - + +
696A ALA* 4.1 21.8 - - + +
697A GLU* 4.3 20.6 - - + +
753A GLU* 4.2 17.0 - - + -
754A VAL* 3.7 26.5 - - + -
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Residues in contact with ARG 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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637A ARG 5.6 2.8 + - - -
638A TYR* 5.4 0.4 - - - +
639A THR 3.1 21.0 + - - +
644A ASP* 3.1 17.5 + - - +
645A PHE* 3.8 27.3 - - - +
647A VAL* 1.3 72.8 - - - +
649A ALA* 1.3 67.1 + - - +
651A ARG* 3.4 30.6 + - - +
652A MET* 3.1 36.1 + - - +
752A GLU* 3.1 41.6 + - - +
753A GLU* 2.8 27.4 + - - +
868A ASP* 4.1 8.7 - - - +
871A LYS* 4.1 16.9 - - - +
1050A TRP* 5.3 9.4 - - + -
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Residues in contact with ALA 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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645A PHE 3.0 15.4 + - - +
646A ASN* 3.3 9.0 - - - +
648A ARG* 1.3 75.1 - - - +
650A GLU* 1.3 60.6 + - - +
652A MET* 3.3 5.4 + - - -
653A GLY 3.3 0.2 + - - -
654A TRP* 2.8 50.2 + - + +
655A LEU* 4.0 15.9 - - + -
1050A TRP* 5.1 1.7 - - + -
1197A MET* 3.9 25.4 - - + +
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Residues in contact with GLU 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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605A MET* 5.7 2.6 - - - +
646A ASN* 2.8 38.7 + - - +
647A VAL* 3.4 12.0 + - - +
649A ALA* 1.3 76.2 - - - +
651A ARG* 1.3 57.8 + - - +
653A GLY* 2.9 21.0 + - - -
655A LEU* 3.6 15.2 - - + +
656A PRO 3.7 13.9 - - - +
657A SER* 2.6 40.5 + - - +
658A ALA 4.9 0.3 + - - -
694A PHE* 4.3 7.8 - - + -
696A ALA* 3.5 30.0 - - + +
883A PRO* 3.8 9.0 - - - +
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Residues in contact with ARG 651 (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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647A VAL* 3.1 22.2 + - + +
648A ARG* 3.4 21.9 - - - +
650A GLU* 1.3 78.5 - - - +
652A MET* 1.3 58.1 + - + +
653A GLY 3.2 1.3 - - - -
694A PHE* 3.8 34.6 - - + -
697A GLU* 4.4 7.7 + - - -
753A GLU* 2.9 43.6 + - - -
868A ASP* 2.8 29.8 + - - -
869A TRP* 2.9 32.5 + - + +
870A LYS* 3.0 47.0 - - - +
871A LYS* 4.2 5.7 - - - +
882A ALA* 3.4 12.3 - - - +
883A PRO* 3.5 2.2 - - - +
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Residues in contact with MET 652 (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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648A ARG* 3.1 26.0 + - - +
649A ALA 3.8 3.4 - - - +
650A GLU 3.1 0.6 - - - -
651A ARG* 1.3 84.0 - - + +
653A GLY* 1.3 62.0 + - - +
654A TRP* 3.3 29.6 + - + -
852A ILE* 3.9 6.1 - - - +
862A GLN* 3.0 24.0 + - - +
866A VAL* 3.3 28.9 - - + -
867A LYS 3.0 28.7 - - - +
868A ASP* 4.3 21.3 - - - +
869A TRP* 5.0 1.8 - - + -
880A LYS 4.6 0.2 - - - +
881A THR* 3.3 24.0 - - - +
882A ALA* 3.5 5.6 + - - -
1050A TRP* 5.8 2.5 - - - -
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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