Contacts of the helix formed by residues 637 - 647 (chain A) in PDB entry 2PTM
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 VAL 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579A GLY 4.9 2.5 - - - +
580A ASP* 2.9 28.5 + - + +
614A LEU* 3.8 31.0 - - + +
617A ARG* 6.3 2.7 - - + -
635A LEU 3.9 0.2 + - - -
636A SER* 1.3 72.3 - - - +
638A GLN* 1.3 83.8 + - - +
640A PHE* 3.5 6.4 - - - +
641A ASN* 3.0 41.3 + - - +
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Residues in contact with GLN 638 (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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580A ASP* 4.2 4.2 + - - +
636A SER* 3.2 26.3 - - - +
637A VAL* 1.3 101.3 - - - +
639A HIS* 1.3 61.6 + - + +
641A ASN* 3.5 5.6 + - - +
642A GLN* 3.0 41.9 + - - +
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Residues in contact with HIS 639 (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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560A LEU* 3.7 48.5 - - + +
562A GLU* 6.3 1.3 - - + -
635A LEU* 3.8 12.8 - - + -
636A SER* 3.0 26.7 + - - +
638A GLN* 1.3 78.2 - - + +
640A PHE* 1.3 67.6 + - - +
642A GLN* 3.3 26.5 + - - +
643A VAL* 2.9 31.2 + - - +
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Residues in contact with PHE 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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582A MET* 3.6 32.8 - - + -
611A GLU* 4.5 2.7 - - + -
614A LEU* 3.6 41.7 - - + -
615A LEU* 3.6 26.2 - - + -
635A LEU* 3.7 18.5 - - + +
636A SER 2.8 21.8 + - - +
637A VAL 3.5 4.3 - - - +
639A HIS* 1.3 72.7 - - - +
641A ASN* 1.3 76.8 + - - +
643A VAL* 3.3 4.0 - - - +
644A LEU* 3.2 51.3 + - + +
651A ARG* 4.8 0.9 - - - -
654A MET* 3.8 20.4 - - + -
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Residues in contact with ASN 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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614A LEU 4.6 5.6 + - - +
617A ARG* 4.3 18.7 + - - +
637A VAL* 3.0 41.8 + - - +
638A GLN* 3.9 4.9 - - - +
640A PHE* 1.3 87.5 - - - +
642A GLN* 1.3 63.1 + - - +
644A LEU* 3.7 0.5 + - - +
645A ASP* 3.2 35.2 + - - +
651A ARG* 3.3 21.7 + - - +
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Residues in contact with GLN 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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560A LEU* 4.4 7.8 - - + +
638A GLN* 3.0 31.5 + - - +
639A HIS* 3.3 31.9 + - - +
641A ASN* 1.3 77.1 - - - +
643A VAL* 1.3 64.7 + - + +
645A ASP* 3.2 6.8 + - - +
646A GLU* 3.0 24.8 + - - +
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Residues in contact with VAL 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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553A PHE* 4.2 18.4 - - + -
556A ARG* 3.7 27.6 - - + -
557A VAL* 4.4 14.4 - - + -
560A LEU* 3.8 15.0 - - + -
635A LEU* 4.3 12.8 - - + -
639A HIS 2.9 14.5 + - - +
640A PHE* 3.3 15.7 - - - +
642A GLN* 1.3 76.9 - - + +
644A LEU* 1.3 73.1 + - + +
646A GLU* 4.4 7.0 - - - -
647A PHE* 2.9 34.9 + - + +
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Residues in contact with LEU 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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553A PHE* 4.7 9.6 - - + -
615A LEU* 4.2 3.4 - - + -
635A LEU* 6.1 0.2 - - + -
640A PHE* 3.2 52.3 + - + +
641A ASN 4.2 0.2 - - - +
642A GLN 3.3 0.2 - - - -
643A VAL* 1.3 93.1 - - + +
645A ASP* 1.3 65.4 + - - +
647A PHE 3.8 3.6 - - - -
648A PRO* 3.3 25.3 - - - +
650A MET 4.7 0.9 - - - -
651A ARG* 3.4 63.2 + - + +
654A MET* 4.3 19.7 - - + -
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Residues in contact with ASP 645 (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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641A ASN* 3.2 21.4 + - - +
642A GLN* 3.2 7.5 + - - +
644A LEU* 1.3 76.8 - - - +
646A GLU* 1.3 66.0 + - - +
647A PHE 3.2 0.4 + - - -
648A PRO* 3.7 13.6 - - - +
651A ARG* 3.9 14.2 + - - -
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Residues in contact with GLU 646 (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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556A ARG* 3.0 47.1 + - - +
642A GLN 3.0 17.4 + - - +
643A VAL* 3.8 1.6 - - - +
645A ASP* 1.3 76.8 - - - +
647A PHE* 1.3 94.2 + - + +
648A PRO* 3.6 6.1 - - - +
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Residues in contact with PHE 647 (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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550A ASP* 4.3 16.6 - - + -
552A ASN* 3.6 23.6 - - + -
553A PHE* 3.4 59.5 - + + -
556A ARG* 4.4 6.7 - - + -
643A VAL* 2.9 21.7 + - + +
644A LEU 3.3 7.4 - - - +
646A GLU* 1.3 115.6 - - + +
648A PRO* 1.3 66.4 - - - +
649A ALA* 3.2 3.1 - - + -
650A MET* 3.0 25.3 + - + +
651A ARG 3.7 1.0 + - - -
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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