Contacts of the helix formed by residues 652 - 658 (chain B) in PDB entry 5FLM
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 652 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B SER 5.5 0.7 - - - -
36B GLU* 4.2 18.4 + - - +
643B LEU* 4.6 9.4 - - - +
646B ARG* 4.6 14.4 - - - +
650B ASN 4.2 3.2 + - - -
651B TYR* 1.3 78.5 - - - +
653B TRP* 1.3 68.0 + - - +
654B GLN* 3.2 11.1 + - - +
655B ASP* 3.0 18.2 + - - +
656B LEU* 3.3 8.3 + - - +
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Residues in contact with TRP 653 (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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29B VAL* 3.7 20.6 - - + -
32B SER* 3.6 41.7 + - - +
33B TYR* 3.7 28.9 - + + -
36B GLU* 3.0 19.1 - - + +
37B LYS* 4.0 15.3 - - + +
529B MET* 4.9 3.4 - - + -
624B PRO* 3.9 24.5 - - + -
652B SER* 1.3 77.8 - - - +
654B GLN* 1.3 61.3 + - - +
656B LEU* 2.9 39.9 + - + +
657B VAL* 2.9 26.0 + - + +
662B VAL* 3.8 28.3 - - + -
664B TYR* 3.3 22.9 + + - -
698B ILE* 5.1 7.2 - - + -
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Residues in contact with GLN 654 (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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36B GLU* 2.8 30.9 + - - +
594B MET* 4.6 12.4 - - + +
652B SER* 3.1 5.9 + - - +
653B TRP* 1.3 78.4 - - - +
655B ASP* 1.3 64.4 + - - +
657B VAL* 3.2 8.4 + - + +
658B ALA* 2.9 26.7 + - + +
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Residues in contact with ASP 655 (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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650B ASN* 3.9 16.5 - - - +
651B TYR* 3.5 41.1 + - + -
652B SER* 3.0 9.6 + - - +
654B GLN* 1.3 81.9 - - - +
656B LEU* 1.3 62.1 + - - +
657B VAL 3.3 0.2 - - - -
658B ALA* 3.7 10.7 - - - +
659B SER* 3.3 21.3 + - - -
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Residues in contact with LEU 656 (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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29B VAL* 4.3 10.3 - - + -
32B SER* 4.6 1.1 - - - +
635B LEU* 4.2 11.4 - - + -
639B HIS* 4.5 4.9 - - - +
643B LEU* 3.9 27.8 - - + -
651B TYR* 4.3 13.8 + - - +
652B SER 3.3 6.5 + - - +
653B TRP* 2.9 44.7 + - + +
655B ASP* 1.3 76.6 - - - +
657B VAL* 1.3 62.0 + - - +
659B SER* 3.6 7.4 + - - +
661B VAL* 3.7 41.9 + - + +
662B VAL* 3.8 16.0 - - + +
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Residues in contact with VAL 657 (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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592B ARG* 3.9 6.8 - - - +
594B MET* 4.4 9.3 - - + +
599B SER* 3.8 23.3 - - - +
653B TRP* 2.9 44.2 + - + +
654B GLN* 3.6 9.0 - - + +
656B LEU* 1.3 75.0 - - - +
658B ALA* 1.3 60.6 + - - +
659B SER 3.1 4.9 - - - -
660B GLY* 3.1 14.0 + - - -
662B VAL* 3.6 29.6 - - + +
663B GLU* 5.8 0.4 - - - -
664B TYR* 4.4 20.2 - - + +
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Residues in contact with ALA 658 (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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592B ARG 4.0 8.5 - - - +
593B GLN* 5.0 6.8 - - - +
594B MET* 3.7 21.7 - - + +
654B GLN* 2.9 16.6 + - + +
655B ASP* 3.6 13.2 + - - +
656B LEU 3.4 0.2 - - - -
657B VAL* 1.3 76.2 - - - +
659B SER* 1.3 58.4 + - - +
660B GLY 3.2 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