Contacts of the helix formed by residues 583 - 596 (chain B) in PDB entry 5F1B
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 SER 583 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572B PHE* 5.6 2.6 - - - -
578B GLU* 4.0 15.9 + - - -
581B THR* 3.7 5.1 - - - +
582B PHE* 1.3 79.4 - - - +
584B ILE* 1.3 59.0 + - - +
585B LEU 3.4 2.5 - - - -
586B ASN* 3.5 15.1 + - - +
587B ARG* 3.0 34.1 + - - +
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Residues in contact with ILE 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.2 13.9 - - + -
97A VAL* 4.0 8.7 - - + -
183A PHE* 3.9 34.1 - - + -
569B LEU* 3.7 30.1 - - + -
572B PHE* 4.0 21.3 - - + -
573B LEU* 5.5 0.2 - - + -
581B THR* 3.6 27.4 - - + -
582B PHE 3.5 2.4 - - - -
583B SER* 1.3 78.0 - - - +
585B LEU* 1.3 59.1 + - + +
587B ARG* 3.3 8.1 + - - +
588B LYS* 2.9 39.7 + - + +
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Residues in contact with LEU 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.9 4.3 - - + -
60A THR* 5.9 0.4 - - - +
63A LEU* 3.3 63.0 - - + +
64A ARG* 4.0 5.4 - - - +
65A SER* 3.9 22.0 - - - +
98A ASN* 6.3 0.7 - - - +
100A GLU* 4.0 11.0 - - - +
183A PHE* 3.9 35.0 - - + -
184A LEU 4.8 1.3 - - - +
582B PHE 4.9 3.0 + - - +
583B SER 3.4 0.4 - - - -
584B ILE* 1.3 73.6 - - + +
586B ASN* 1.3 68.4 + - - +
588B LYS* 3.2 7.3 + - + +
589B ALA 3.0 17.5 + - - -
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Residues in contact with ASN 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 3.5 20.3 + - - +
582B PHE 5.2 3.8 + - - -
583B SER* 3.5 18.7 + - - +
584B ILE 3.4 0.4 - - - -
585B LEU* 1.3 78.4 - - - +
587B ARG* 1.3 63.1 + - - +
589B ALA* 3.2 7.9 + - - +
590B ILE* 3.0 30.5 + - + +
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Residues in contact with ARG 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B PHE* 3.8 30.2 - - - -
583B SER* 3.0 23.5 + - - +
584B ILE* 3.5 7.6 - - - +
585B LEU 3.2 0.2 - - - -
586B ASN* 1.3 74.3 - - - +
588B LYS* 1.3 65.8 + - + +
590B ILE* 3.3 12.9 + - + +
591B ASP* 3.0 38.5 + - - +
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Residues in contact with LYS 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 5.1 2.2 - - - -
33A ILE* 2.9 49.1 + - - +
35A LEU* 4.6 30.5 - - + -
47A ASP* 3.5 23.9 + - - +
48A VAL* 4.3 10.3 - - + +
57A LEU* 5.8 0.2 - - - -
63A LEU* 5.1 4.9 - - + -
183A PHE* 6.1 1.8 - - + -
584B ILE* 2.9 28.8 + - + +
585B LEU* 3.2 14.6 + - + +
587B ARG* 1.3 77.0 - - + +
589B ALA* 1.3 57.2 + - - +
591B ASP* 3.2 10.7 + - - +
592B PHE* 2.9 29.3 + - - +
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Residues in contact with ALA 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 4.5 13.7 - - + -
60A THR* 4.7 9.0 - - - +
63A LEU* 3.9 14.9 - - + +
585B LEU 3.0 12.7 + - - +
586B ASN* 3.2 12.8 + - - +
588B LYS* 1.3 76.1 - - - +
590B ILE* 1.3 61.7 + - + +
592B PHE* 3.4 9.7 - - - +
593B LEU* 3.2 29.5 + - + +
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Residues in contact with ILE 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586B ASN* 3.0 18.2 + - + +
587B ARG* 3.6 14.6 - - + +
589B ALA* 1.3 76.3 - - + +
591B ASP* 1.3 55.3 + - - +
593B LEU* 3.0 12.9 + - + +
594B LEU* 2.8 54.8 + - + +
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Residues in contact with ASP 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 4.3 17.3 - - + +
587B ARG* 3.0 33.5 + - - +
588B LYS* 3.2 14.7 + - + +
590B ILE* 1.3 77.1 - - - +
592B PHE* 1.3 53.5 + - - +
594B LEU* 3.8 18.5 - - - +
595B GLN* 2.8 35.0 + - - +
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Residues in contact with PHE 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.6 28.8 - - + +
51A LEU* 3.9 32.5 - - + -
52A VAL 5.7 0.4 - - - -
55A ASP 4.2 17.9 - - - -
57A LEU* 3.9 45.3 - - + -
588B LYS 2.9 12.2 + - - +
589B ALA* 3.4 15.0 - - - +
591B ASP* 1.3 78.2 - - - +
593B LEU* 1.3 77.9 + - + +
595B GLN* 3.4 5.7 - - + +
596B ARG* 3.4 28.5 + - + +
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Residues in contact with LEU 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589B ALA* 3.2 19.3 + - + +
590B ILE* 3.0 13.2 + - + +
592B PHE* 1.3 93.5 - - + +
594B LEU* 1.3 63.5 + - + +
596B ARG* 3.4 1.9 + - - +
597B TRP* 3.1 35.7 + - + +
598B GLY 3.7 0.2 + - - -
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Residues in contact with LEU 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B ILE* 2.8 40.5 + - + +
591B ASP* 3.3 18.8 + - - +
593B LEU* 1.3 69.6 - - + +
595B GLN* 1.3 65.4 + - - +
598B GLY* 2.9 37.3 + - - +
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Residues in contact with GLN 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.8 24.9 - - + +
49A ASP* 5.3 4.5 - - - -
591B ASP 2.8 14.7 + - - +
592B PHE* 3.4 13.7 - - + +
594B LEU* 1.3 79.5 + - - +
596B ARG* 1.3 92.9 + - + +
597B TRP 3.7 1.7 + - - -
598B GLY 4.6 0.3 + - - -
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Residues in contact with ARG 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL 5.1 5.0 + - - -
50A LYS* 5.0 7.9 + - - +
51A LEU 4.3 17.9 + - - +
52A VAL* 5.6 1.0 - - - +
53A CYS* 4.3 33.2 - - - +
592B PHE* 3.4 20.9 + - + +
593B LEU* 3.7 1.6 - - - -
594B LEU 3.4 0.4 - - - -
595B GLN* 1.3 120.6 + - + +
597B TRP* 1.3 63.2 + - - +
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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