Contacts of the helix formed by residues 630 - 638 (chain B) in PDB entry 1FM9
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A VAL* 3.8 18.7 - - + +
302A ARG* 3.1 54.3 + - - -
453A GLU* 3.2 27.1 - - + +
454A MET* 6.3 0.9 - - - -
456A GLU* 3.9 25.1 + - + -
631B LYS* 1.3 68.1 + - - +
632B ILE 3.4 0.2 + - - -
633B LEU* 3.4 10.9 + - + -
634B HIS* 2.8 28.7 + - + +
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Residues in contact with LYS 631 (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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453A GLU* 3.6 6.4 + - - +
630B HIS* 1.3 71.3 - - - +
632B ILE* 1.3 58.0 + - + +
634B HIS* 3.8 2.7 - - - +
635B ARG* 2.8 40.2 + - - +
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Residues in contact with ILE 632 (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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277A PHE* 4.1 11.0 - - + -
449A THR* 3.3 35.4 - - + -
450A PHE* 3.7 43.7 - - + +
453A GLU* 3.0 17.9 + - - +
631B LYS* 1.3 79.2 - - + +
633B LEU* 1.3 57.5 + - - +
635B ARG* 3.6 4.3 - - - +
636B LEU* 2.8 50.6 + - + +
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Residues in contact with LEU 633 (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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280A VAL* 4.0 22.7 - - + -
298A VAL* 3.3 51.8 - - + +
301A LEU* 4.0 15.7 - - + -
302A ARG* 4.9 2.2 - - + -
450A PHE* 3.9 18.8 - - + -
453A GLU* 3.0 15.0 + - - +
454A MET* 4.8 13.7 - - + -
630B HIS* 4.1 5.6 - - + +
632B ILE* 1.3 78.7 - - - +
634B HIS* 1.3 63.0 + - - +
636B LEU* 3.5 1.5 + - - +
637B LEU* 3.1 39.8 + - + +
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Residues in contact with HIS 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 3.4 31.6 - - + +
295A ASP* 4.5 9.4 + - - -
298A VAL* 4.2 13.5 - - + -
630B HIS* 2.8 29.9 + - + +
631B LYS* 3.8 2.5 - - - +
633B LEU* 1.3 81.0 - - - +
635B ARG* 1.3 61.3 + - - +
637B LEU* 3.5 2.8 + - - +
638B GLN* 3.0 55.4 + - - +
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Residues in contact with ARG 635 (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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631B LYS 2.8 24.4 + - - +
632B ILE* 3.6 5.4 - - - +
634B HIS* 1.3 72.6 + - - +
636B LEU* 1.3 84.7 + - - +
637B LEU 3.3 0.5 + - - -
638B GLN* 3.4 30.5 + - + +
639B GLU* 3.6 32.3 + - - +
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Residues in contact with LEU 636 (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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277A PHE* 3.7 25.6 - - + +
280A VAL* 3.9 22.6 - - + +
284A LYS* 2.8 23.6 + - - -
450A PHE* 3.6 35.7 - - + -
632B ILE* 2.8 32.9 + - + +
633B LEU 4.0 2.9 - - - +
635B ARG* 1.3 94.3 - - + +
637B LEU* 1.3 59.9 + - - +
639B GLU* 3.4 19.1 - - - +
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Residues in contact with LEU 637 (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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280A VAL* 3.8 22.4 - - + -
284A LYS* 3.9 20.6 - - + +
289A PHE* 4.1 6.7 - - + -
294A LEU* 4.8 11.9 - - + +
297A GLN* 3.6 27.5 - - + +
298A VAL* 3.9 23.3 - - + +
301A LEU* 4.0 16.4 - - + -
633B LEU* 3.1 49.4 + - + +
634B HIS* 3.9 4.7 - - - +
635B ARG 3.2 0.4 - - - -
636B LEU* 1.3 77.6 - - - +
638B GLN* 1.3 56.8 + - - +
639B GLU 3.5 5.6 + - - +
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Residues in contact with GLN 638 (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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294A LEU* 3.7 20.7 - - + +
634B HIS* 3.0 44.5 + - - +
635B ARG* 3.4 23.4 + - + +
637B LEU* 1.3 75.7 - - - +
639B GLU* 1.4 56.9 + - + +
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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