Contacts of the helix formed by residues 639 - 644 (chain A) in PDB entry 3THW
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 639 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ALA 5.7 2.5 - - - -
310A LEU* 6.1 1.8 - - - -
311A ASN* 5.6 5.7 + - - +
638A ARG* 1.3 71.8 - - - +
640A ALA* 1.3 66.7 - - - +
641A CYS* 3.6 16.0 - - + +
642A VAL* 3.3 42.7 - - + +
643A GLU* 2.9 27.6 + - - +
650A PHE* 3.3 23.9 - - + -
677A THR* 3.8 10.8 + - + +
680A ARG* 4.2 14.1 - - + -
681A GLN* 3.3 41.9 + - + +
684A VAL* 4.2 16.9 - - + +
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Residues in contact with ALA 640 (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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326A LEU* 4.6 0.9 - - + -
329A LEU* 3.9 23.8 - - + +
619A TYR* 4.2 4.9 + - - +
638A ARG 3.3 5.1 + - - -
639A HIS* 1.3 74.6 - - - +
641A CYS* 1.3 64.9 + - - +
643A GLU* 3.8 10.5 - - - +
644A VAL* 3.5 16.1 - - - +
684A VAL* 4.2 14.8 - - + +
685A ILE* 5.5 0.6 - - - +
688A MET* 4.1 17.3 - - - -
696A PRO* 4.0 26.0 - - + +
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Residues in contact with CYS 641 (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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310A LEU 5.9 1.1 - - - -
311A ASN* 5.2 3.6 - - - -
323A SER* 6.1 1.6 - - - -
324A GLN* 3.6 33.0 - - + +
325A SER 4.0 4.9 - - - -
326A LEU* 3.9 28.3 - - - -
329A LEU* 4.3 14.1 - - + -
639A HIS* 3.3 14.6 - - + +
640A ALA* 1.3 77.3 - - - +
642A VAL* 1.3 68.2 + - + +
643A GLU 3.1 1.6 - - - -
644A VAL* 3.1 27.3 + - - +
645A GLN* 3.8 7.0 + - - -
684A VAL* 5.9 3.1 - - - -
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Residues in contact with VAL 642 (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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323A SER* 6.2 3.4 - - - -
639A HIS* 3.3 36.4 + - + +
641A CYS* 1.3 74.9 - - + +
643A GLU* 1.3 66.2 + - - +
645A GLN* 3.0 32.8 + - + +
648A ILE* 3.5 23.3 - - + +
650A PHE* 3.7 17.9 - - + -
677A THR* 4.9 9.0 - - + -
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Residues in contact with GLU 643 (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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616A PRO* 4.1 26.2 - - + +
617A VAL* 3.7 14.4 - - - +
619A TYR* 4.2 12.1 + - - -
638A ARG* 2.9 52.7 + - + +
639A HIS 2.9 20.3 + - - +
640A ALA* 3.8 11.0 - - - +
642A VAL* 1.3 78.7 - - - +
644A VAL* 1.3 58.6 + - + +
645A GLN 3.5 2.3 + - - -
648A ILE 4.4 8.0 - - - +
650A PHE* 4.3 22.0 + - + +
696A PRO* 4.8 0.7 - - - +
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Residues in contact with VAL 644 (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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324A GLN* 5.3 1.3 - - - +
329A LEU* 3.8 21.3 - - + -
616A PRO* 3.6 34.5 - - + -
619A TYR* 5.9 0.7 - - - +
640A ALA 3.5 15.3 - - - +
641A CYS 3.2 17.3 - - - +
643A GLU* 1.3 73.8 - - + +
645A GLN* 1.3 66.6 + - - +
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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