Contacts of the helix formed by residues 605 - 614 (chain S) in PDB entry 4US1
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 THR 605 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584S GLU 4.3 2.7 - - - +
585S ASN* 3.0 25.4 + - + +
604S GLY* 1.3 76.3 - - - -
606S VAL* 1.3 59.0 + - - +
607S ILE* 3.8 10.4 + - - +
608S LYS* 3.2 26.4 + - - +
609S LEU* 2.8 26.5 + - - +
953S LYS* 6.1 0.9 - - + -
954S GLU 4.2 8.5 - - - +
955S LEU* 3.6 22.4 - - + +
956S ILE* 4.2 2.7 - - - +
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Residues in contact with VAL 606 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576S ARG* 6.0 1.3 - - - +
605S THR* 1.3 73.3 - - - +
607S ILE* 1.4 66.0 + - + +
609S LEU* 3.1 4.2 + - + +
610S ILE* 2.8 56.7 + - + +
634S PHE* 4.4 8.3 - - + +
635S CYS* 4.4 20.0 - - + -
643S LEU* 4.0 22.0 - - + -
956S ILE* 3.7 25.4 - - + +
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Residues in contact with ILE 607 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576S ARG* 3.5 68.4 - - + +
577S PHE* 3.5 34.5 - - + -
579S GLU* 6.2 0.2 - - + -
605S THR* 3.2 9.7 + - - +
606S VAL* 1.4 85.8 - - + +
608S LYS* 1.4 57.4 + - + +
610S ILE* 3.4 1.7 + - - -
611S GLU* 2.8 32.5 + - + +
643S LEU* 5.4 4.9 - - + -
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Residues in contact with LYS 608 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576S ARG 5.9 0.4 - - - -
577S PHE 5.4 0.9 - - - -
579S GLU* 2.8 31.3 + - - -
580S PRO* 4.1 0.9 - - - +
581S ASP* 2.8 31.1 + - - +
585S ASN* 3.5 46.4 - - + +
586S ILE* 4.0 18.2 - - + -
604S GLY* 4.8 0.7 - - - -
605S THR* 3.2 19.5 + - - +
607S ILE* 1.4 79.3 - - + +
609S LEU* 1.4 61.2 + - - +
611S GLU* 2.8 31.3 + - - +
612S ARG* 3.1 34.3 + - + +
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Residues in contact with LEU 609 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586S ILE* 5.5 0.9 - - + -
601S ILE* 3.9 29.6 - - + -
604S GLY* 4.2 14.8 - - - +
605S THR 2.8 16.4 + - - +
606S VAL* 3.1 7.2 + - - +
608S LYS* 1.4 75.7 - - + +
610S ILE* 1.4 58.9 + - - +
612S ARG* 3.2 2.0 + - - -
613S LEU* 2.9 29.1 + - - +
623S PHE* 3.4 19.1 - - + -
627S PHE* 4.1 13.7 - - + -
634S PHE* 4.1 11.9 - - + -
956S ILE* 4.1 33.7 - - + +
958S PHE* 3.9 26.2 - - + -
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Residues in contact with ILE 610 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577S PHE* 3.4 31.0 - - + -
606S VAL* 2.8 49.8 + - + +
607S ILE* 3.8 2.9 - - - +
609S LEU* 1.4 68.9 - - - +
611S GLU* 1.4 57.3 + - - +
613S LEU* 3.2 9.3 + - + +
614S THR* 2.7 33.3 + - + +
627S PHE* 4.0 18.8 - - + -
635S CYS* 5.6 0.4 - - - -
640S LEU* 4.1 16.6 - - + -
643S LEU* 3.8 34.1 - - + +
644S ILE* 4.5 9.2 - - + -
647S ARG* 4.2 10.3 - - + -
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Residues in contact with GLU 611 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577S PHE* 3.4 27.8 - - + +
579S GLU 5.2 0.2 - - - -
581S ASP* 5.0 2.6 - - - +
607S ILE* 2.8 21.3 + - + +
608S LYS* 2.8 42.8 + - - +
609S LEU 3.3 0.2 - - - -
610S ILE* 1.4 71.7 - - - +
612S ARG* 1.3 60.8 - - - +
614S THR 3.0 29.6 - - - +
615S TYR* 3.0 29.5 + - + -
616S HIS* 5.0 4.0 - - - -
647S ARG* 3.6 26.2 + - - +
681S TYR* 4.7 5.6 + - - +
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Residues in contact with ARG 612 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581S ASP* 2.7 35.0 + - - -
586S ILE* 3.8 9.5 - - + +
588S PHE* 3.6 29.2 - - - -
599S PRO* 4.0 7.7 - - - +
601S ILE* 3.5 31.1 - - + +
608S LYS* 3.1 16.3 + - + +
609S LEU 3.2 3.8 + - - +
611S GLU* 1.3 81.4 + - + +
613S LEU* 1.3 61.1 + - - +
614S THR 3.3 0.4 - - - -
615S TYR* 3.5 56.4 + - - +
618S TYR* 3.6 21.4 + - - -
620S ASP* 4.4 14.1 - - - +
623S PHE* 3.6 12.9 - - + -
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Residues in contact with LEU 613 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609S LEU 2.9 15.7 + - - +
610S ILE* 3.2 11.2 + - + +
612S ARG* 1.3 76.5 - - - +
614S THR* 1.3 60.7 + - + +
615S TYR 3.7 1.2 + - - -
620S ASP* 5.8 2.0 + - - +
623S PHE* 3.5 9.8 - - + -
624S VAL* 3.7 42.2 - - + +
627S PHE* 3.5 55.0 - - + -
628S LEU* 5.4 0.9 - - + -
640S LEU* 4.6 1.8 - - + -
644S ILE* 4.6 13.7 - - + -
688S ARG* 4.6 5.7 - - - +
692S VAL* 3.7 32.9 - - + +
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Residues in contact with THR 614 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610S ILE 2.7 15.6 + - - +
611S GLU 3.0 2.4 + - - -
613S LEU* 1.3 86.3 - - + +
615S TYR* 1.4 60.2 + - - +
644S ILE* 5.0 5.8 - - + -
647S ARG* 2.7 55.3 + - + +
685S VAL* 3.8 9.5 - - - +
688S ARG* 3.7 17.9 - - - -
689S VAL* 3.6 37.9 - - + +
692S VAL* 3.9 10.1 - - + -
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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