Contacts of the helix formed by residues 675 - 683 (chain A) in PDB entry 4F1P
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 ASP 675 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645A HIS* 3.9 2.5 - - - -
666A LEU 3.9 9.0 - - - +
667A GLY* 4.3 6.4 - - - -
668A ALA 3.2 10.3 - - - +
669A ARG* 3.3 35.6 + - + +
674A ARG* 1.3 74.5 - - - +
676A PRO* 1.3 76.9 - - + +
677A LEU* 3.8 12.9 - - - +
678A THR* 2.5 43.3 + - - -
679A ILE* 3.3 10.6 + - - +
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Residues in contact with PRO 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A LEU* 3.8 33.7 - - + -
645A HIS* 3.7 20.4 - - + +
648A THR* 3.3 27.2 - - + +
665A ASP 4.7 2.7 - - - +
666A LEU 3.3 22.7 - - - +
668A ALA 3.5 11.4 - - - +
675A ASP* 1.3 82.9 - - + +
677A LEU* 1.3 55.7 + - - +
679A ILE* 3.3 4.6 + - + +
680A ALA* 2.9 24.9 + - - +
692A LEU* 3.6 14.4 - - + -
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Residues in contact with LEU 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A LEU* 5.3 1.4 + - + +
675A ASP* 3.2 13.7 + - - +
676A PRO* 1.3 77.1 - - - +
678A THR* 1.3 58.1 + - - +
680A ALA* 3.2 2.3 + - - +
681A MET* 2.8 37.4 + - + +
689A VAL* 3.9 40.6 - - + +
692A LEU* 3.6 20.8 - - + +
693A ARG* 4.1 26.2 - - + +
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Residues in contact with THR 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A ARG* 4.0 8.6 + - - +
673A GLY 5.6 0.2 - - - +
674A ARG* 4.2 13.2 - - + -
675A ASP* 2.5 35.7 + - - -
677A LEU* 1.3 77.2 - - - +
679A ILE* 1.3 55.6 + - - +
681A MET* 3.3 6.5 + - + +
682A GLU* 2.9 51.5 + - + +
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Residues in contact with ILE 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A HIS* 3.5 38.1 - - + +
648A THR* 3.8 14.1 - - + -
649A ILE* 3.8 35.4 - - + +
670A ASP* 4.1 1.1 - - - +
674A ARG* 3.9 42.2 - - + +
675A ASP 3.3 7.1 + - - +
676A PRO* 3.3 7.5 + - + +
677A LEU 3.3 0.2 - - - -
678A THR* 1.3 75.7 - - - +
680A ALA* 1.3 52.4 + - - +
682A GLU* 3.4 6.9 + - - -
683A THR* 2.8 46.3 + - + +
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Residues in contact with ALA 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A THR* 3.5 14.7 - - + +
676A PRO 2.9 17.4 + - - +
677A LEU 3.2 5.1 + - - +
679A ILE* 1.3 76.4 - - - +
681A MET* 1.3 59.1 + - - +
683A THR* 3.2 8.5 + - - -
685A ASN* 3.0 30.1 + - - +
688A ILE* 3.9 4.5 - - + -
689A VAL* 3.6 31.7 - - + +
692A LEU* 3.9 9.0 - - + -
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Residues in contact with MET 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A LEU* 2.8 29.3 + - + +
678A THR* 3.7 6.5 - - - +
680A ALA* 1.3 73.9 - - - +
682A GLU* 1.3 58.3 + - + +
684A ALA* 3.0 21.4 + - - +
689A VAL* 3.4 36.8 - - + -
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Residues in contact with GLU 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A ARG* 3.7 28.0 + - - +
678A THR* 2.9 37.0 + - + +
679A ILE* 3.4 7.4 + - + +
681A MET* 1.3 74.5 - - + +
683A THR* 1.3 60.6 + - + +
684A ALA* 3.2 1.6 + - - +
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Residues in contact with THR 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A THR 4.3 6.3 + - - +
649A ILE* 4.5 15.9 - - + +
679A ILE* 2.8 37.0 + - + +
680A ALA* 3.2 12.3 + - - -
681A MET 3.2 0.2 - - - -
682A GLU* 1.3 78.3 - - + +
684A ALA* 1.3 68.1 + - - +
685A ASN* 3.3 13.2 + - - +
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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