Contacts of the helix formed by residues 675 - 682 (chain A) in PDB entry 4FYT
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 PRO 675 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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636A GLU* 3.6 28.3 - - - +
674A VAL* 1.3 92.8 - - + +
676A VAL* 1.3 65.4 + - - +
677A THR* 4.0 6.3 - - - +
678A LEU* 3.0 23.3 + - + +
679A ALA 3.6 3.3 + - - -
1E NAG 3.8 25.6 - - + -
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Residues in contact with VAL 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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669A ALA* 3.8 21.7 + - + +
674A VAL 3.5 2.6 + - - -
675A PRO* 1.3 73.1 - - - +
677A THR* 1.3 60.2 + - + +
679A ALA* 3.2 5.2 + - + +
680A LEU* 2.9 30.0 + - + +
705A PHE* 3.7 30.5 - - + -
950A TRP* 4.5 4.9 - - + +
954A ASN* 3.3 27.1 + - - +
957A VAL* 3.6 29.8 - - + -
958A VAL* 4.0 14.1 - - + -
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Residues in contact with THR 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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675A PRO* 4.0 5.1 - - + +
676A VAL* 1.3 78.7 - - + +
678A LEU* 1.3 55.6 + - - +
680A LEU* 4.4 2.2 - - - +
681A ASN* 2.8 36.0 + - - +
957A VAL* 3.6 29.4 - - + -
961A TRP* 3.7 32.9 + - + -
1E NAG 3.2 32.0 + - - +
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Residues in contact with LEU 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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636A GLU* 4.0 25.4 - - + +
639A TRP* 3.7 55.4 - - + +
640A ARG* 6.2 1.6 - - + -
643A GLN* 3.4 24.4 + - - +
665A ALA* 4.2 6.5 - - + -
674A VAL* 4.5 11.7 - - + -
675A PRO* 3.0 14.1 + - + +
677A THR* 1.3 79.5 + - - +
679A ALA* 1.3 65.1 - - - +
681A ASN* 3.3 1.1 + - - -
682A ASN* 3.1 33.0 + - - +
1E NAG 3.7 20.4 - - + +
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Residues in contact with ALA 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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665A ALA* 3.5 41.3 - - - +
666A PHE* 3.7 35.9 - - + +
669A ALA* 4.3 8.3 - - + -
674A VAL* 4.9 0.4 - - - +
675A PRO 3.6 2.0 + - - +
676A VAL* 3.2 8.8 + - - +
678A LEU* 1.3 81.0 - - - +
680A LEU* 1.3 62.4 + - - +
682A ASN* 3.2 17.2 + - - +
683A THR 3.8 1.7 + - - -
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Residues in contact with LEU 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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666A PHE* 3.9 24.5 - - + -
676A VAL* 2.9 34.6 + - + +
677A THR* 4.0 1.8 - - - +
679A ALA* 1.3 74.7 - - - +
681A ASN* 1.3 58.3 + - - +
683A THR* 2.7 34.2 + - + +
684A LEU 3.8 0.9 + - - -
702A LEU* 4.4 3.4 - - + -
705A PHE* 4.1 6.5 - - + -
721A TYR* 5.6 0.4 - - + -
958A VAL* 4.4 16.4 - - + -
961A TRP* 3.4 53.0 - - + -
962A PHE* 3.8 31.9 - - + -
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Residues in contact with ASN 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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643A GLN* 3.6 21.5 + - - +
677A THR 2.8 16.1 + - - +
678A LEU* 3.3 6.0 + - - +
680A LEU* 1.3 77.6 - - - +
682A ASN* 1.3 60.8 + - - +
683A THR 3.1 1.3 + - - -
684A LEU* 3.2 32.3 + - + +
685A PHE 4.8 0.5 + - - -
961A TRP* 2.9 26.0 + - - -
965A ASN* 4.9 0.9 - - - +
1E NAG 1.4 65.1 + - - +
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Residues in contact with ASN 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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639A TRP* 3.6 11.2 - - - -
642A ILE* 5.5 0.3 - - - +
643A GLN* 2.8 32.2 + - - +
646A LEU* 4.5 4.4 - - - +
661A ILE* 3.3 34.5 + - + +
662A ILE* 3.8 12.0 - - + +
665A ALA* 3.2 30.1 - - - +
678A LEU* 3.1 16.6 + - - +
679A ALA* 3.4 9.2 - - - +
680A LEU 3.2 0.4 - - - -
681A ASN* 1.3 74.4 - - - +
683A THR* 1.3 59.1 + - - +
684A LEU 3.4 0.7 - - - -
685A PHE* 3.2 29.7 - - - -
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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