Contacts of the helix formed by residues 581 - 587 (chain B) in PDB entry 1FO4
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 ALA 581 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579B HIS* 2.9 22.1 + - + -
580B LEU* 1.3 76.5 - - - +
582B ALA* 1.3 65.0 + - - +
583B ALA 3.3 2.7 - - - -
584B MET* 3.2 19.9 + - + -
585B GLN* 2.9 34.6 + - + +
793B ARG* 3.8 23.8 - - - +
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Residues in contact with ALA 582 (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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106B ALA* 3.8 31.2 - - + +
109B HIS* 6.2 0.4 - - - -
111B SER* 4.5 13.1 + - - +
578B PRO* 5.0 2.0 - - + -
579B HIS* 3.1 30.2 + - + +
580B LEU 3.5 0.4 - - - -
581B ALA* 1.3 77.2 - - - +
583B ALA* 1.3 58.0 + - - +
585B GLN* 3.3 12.3 + - - +
586B ALA* 2.8 31.2 + - - +
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Residues in contact with ALA 583 (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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94B THR* 3.8 19.9 - - + +
98B LEU* 4.0 19.9 - - + +
106B ALA* 3.9 12.6 - - + +
580B LEU 5.0 2.8 + - - +
581B ALA 3.3 0.6 - - - -
582B ALA* 1.3 77.7 - - - +
584B MET* 1.3 59.2 + - + +
586B ALA* 3.3 3.5 + - - +
587B SER* 3.0 28.9 + - - -
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Residues in contact with MET 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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755A GLY 4.8 0.7 - - - +
756A GLU* 3.6 45.8 - - + +
757A GLU* 3.7 35.0 - - + +
94B THR* 4.1 20.6 - - + +
580B LEU 4.2 3.4 - - - +
581B ALA* 3.2 31.8 + - + +
583B ALA* 1.3 74.7 - - + +
585B GLN* 1.3 60.3 + - - +
587B SER* 3.4 7.2 - - - -
588B GLY 3.0 6.1 + - - -
589B GLU* 2.8 33.6 + - + -
590B ALA* 3.0 18.7 + - + +
793B ARG* 5.0 0.4 - - - +
1062B TYR* 5.6 0.4 - - - +
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Residues in contact with GLN 585 (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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111B SER* 2.9 30.7 + - - +
112B GLN 3.2 21.5 + - - +
113B CYS* 3.2 18.2 - - - +
114B GLY* 3.5 10.5 - - - +
117B THR* 3.6 5.5 - - - -
118B PRO* 3.6 18.7 - - - +
579B HIS* 3.7 7.9 + - - -
581B ALA* 2.9 33.4 + - + +
582B ALA* 3.6 9.1 - - - +
584B MET* 1.3 77.3 - - - +
586B ALA* 1.3 62.6 + - - +
587B SER 3.3 0.3 + - - -
588B GLY* 3.3 8.5 + - - -
590B ALA* 3.7 15.0 - - + -
592B TYR* 3.7 12.6 + - - +
793B ARG* 4.1 7.8 + - - -
1037B GLU* 6.0 0.3 - - - +
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Residues in contact with ALA 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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88B VAL* 3.3 16.4 - - - +
102B GLN* 3.3 43.4 + - + +
105B ILE* 3.7 18.4 - - + -
106B ALA* 4.4 2.2 - - + -
117B THR* 3.3 12.5 - - + +
118B PRO* 4.9 0.4 - - - +
121B VAL* 3.7 5.7 - - - +
582B ALA 2.8 17.4 + - - +
583B ALA* 3.3 5.4 + - - +
585B GLN* 1.3 77.6 - - - +
587B SER* 1.3 58.1 + - - +
588B GLY 3.4 0.2 - - - -
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Residues in contact with SER 587 (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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88B VAL* 3.5 16.2 - - - +
89B GLU* 4.2 13.2 + - - +
92B GLY 4.4 0.7 - - - +
93B SER* 4.0 17.9 - - - -
98B LEU* 4.1 8.5 - - - -
102B GLN* 3.6 9.2 - - - +
583B ALA 3.0 15.0 + - - -
584B MET* 3.1 12.0 + - - -
585B GLN 3.1 0.2 - - - -
586B ALA* 1.3 76.1 - - - +
588B GLY* 1.3 60.8 + - - +
589B GLU* 2.5 36.8 + - - +
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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