Contacts of the helix formed by residues 630 - 639 (chain V) in PDB entry 1FM6
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 630 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298U VAL* 4.0 13.2 - - + +
302U ARG* 3.1 54.7 + - - +
453U GLU* 3.4 32.5 - - + +
454U MET* 6.3 0.2 - - + -
456U GLU* 5.2 6.3 - - + +
628V GLU* 4.0 30.0 + - + +
629V ARG* 1.3 80.8 + - - +
631V LYS* 1.3 58.3 + - - +
632V ILE 3.5 0.2 - - - -
633V LEU* 4.3 9.6 - - + -
634V HIS* 2.9 32.6 + - - +
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Residues in contact with LYS 631 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453U GLU* 3.1 6.4 + - - +
629V ARG* 4.7 32.3 - - - +
630V HIS* 1.3 67.7 - - - +
632V ILE* 1.3 60.0 + - + +
634V HIS* 3.3 3.7 + - - +
635V ARG* 2.7 60.7 + - - +
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Residues in contact with ILE 632 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277U PHE* 4.3 8.1 - - + -
449U THR* 3.7 40.4 - - - +
450U PHE* 3.7 35.4 - - + -
453U GLU* 3.0 18.8 + - + +
631V LYS* 1.3 74.0 - - + +
633V LEU* 1.3 63.0 + - - +
635V ARG* 3.7 17.2 - - - +
636V LEU* 3.0 39.7 + - + +
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Residues in contact with LEU 633 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280U VAL* 4.4 11.9 - - + -
298U VAL* 3.2 51.8 - - + +
301U LEU* 4.1 13.9 - - + -
302U ARG* 4.0 4.3 - - + -
450U PHE* 4.1 8.7 - - + -
453U GLU* 3.2 16.1 + - - +
454U MET* 3.2 31.9 - - + -
630V HIS* 3.5 5.8 + - + +
631V LYS 3.3 0.2 - - - -
632V ILE* 1.3 78.1 - - - +
634V HIS* 1.3 57.5 + - - +
636V LEU* 3.9 1.2 - - - +
637V LEU* 2.9 46.7 + - + +
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Residues in contact with HIS 634 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294U LEU* 3.5 31.9 - - + +
295U ASP* 4.7 9.0 + - - -
298U VAL* 4.3 17.2 - - + +
629V ARG* 3.9 35.6 + - - +
630V HIS 2.9 21.7 + - - +
631V LYS 3.9 2.0 - - - +
633V LEU* 1.3 74.4 - - - +
635V ARG* 1.3 66.6 + - - +
637V LEU* 4.2 1.7 - - - +
638V GLN* 3.1 47.6 + - - +
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Residues in contact with ARG 635 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631V LYS* 2.7 48.9 + - - +
632V ILE* 3.7 23.5 - - - +
634V HIS* 1.3 78.0 + - - +
636V LEU* 1.3 71.8 + - + +
638V GLN* 3.9 4.8 - - - +
639V GLU* 3.1 23.6 + - + +
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Residues in contact with LEU 636 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277U PHE* 3.9 30.3 - - + +
280U VAL* 3.9 25.6 - - + -
281U GLU* 5.2 1.8 - - - +
284U LYS* 3.5 4.9 - - - -
450U PHE* 4.0 16.4 - - + -
632V ILE* 3.0 28.8 + - + +
633V LEU 4.0 2.0 - - - +
635V ARG* 1.3 90.5 - - + +
637V LEU* 1.3 67.8 + - - +
639V GLU* 3.0 46.0 + - - +
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Residues in contact with LEU 637 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280U VAL* 4.1 11.2 - - + +
284U LYS* 2.6 31.2 + - + +
289U PHE* 3.9 15.5 - - + -
294U LEU* 4.2 8.6 - - + +
297U GLN* 3.1 39.2 + - + +
298U VAL* 3.4 45.3 - - + +
301U LEU* 4.1 10.3 - - + -
633V LEU* 2.9 31.1 + - + +
634V HIS* 4.2 2.7 - - - +
636V LEU* 1.3 76.0 - - - +
638V GLN* 1.3 59.3 + - - +
639V GLU 3.4 0.2 - - - +
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Residues in contact with GLN 638 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294U LEU* 3.9 25.6 - - + +
634V HIS* 3.1 38.6 + - + +
635V ARG* 4.0 4.2 - - - +
637V LEU* 1.3 76.3 - - - +
639V GLU* 1.3 65.5 + - - +
640V GLY 3.7 0.9 + - - -
641V SER* 4.9 4.0 + - - -
642V PRO* 5.0 2.1 - - - +
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Residues in contact with GLU 639 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281U GLU* 3.6 20.9 - - - +
284U LYS* 3.1 27.2 + - - -
635V ARG* 3.1 13.0 + - + +
636V LEU* 3.0 38.4 + - - +
637V LEU 3.4 0.2 - - - +
638V GLN* 1.3 78.7 - - - +
640V GLY* 1.3 61.0 + - - +
642V PRO* 4.2 15.3 - - + -
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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