Contacts of the helix formed by residues 687 - 695 (chain A) in PDB entry 4PE5
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 SER 687 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A PHE* 4.3 3.1 - - - -
486A THR* 4.1 0.2 - - - -
523A ARG* 3.7 12.3 - - - +
683A THR* 3.8 2.8 + - - -
684A VAL* 2.4 31.4 + - - -
686A GLN* 1.3 76.1 - - - +
688A SER* 1.3 60.8 + - - +
689A VAL 3.7 0.9 + - - -
690A ASP* 3.1 13.3 + - - +
691A ILE* 3.0 29.8 + - - +
731A TRP* 3.5 33.2 - - - -
942A GLY* 4.2 2.7 - - - -
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Residues in contact with SER 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A THR* 3.2 27.9 + - - -
520A ASN* 5.1 6.6 + - - +
523A ARG* 2.6 35.3 + - - +
538A LEU* 5.3 3.5 - - - +
687A SER* 1.3 72.9 - - - +
689A VAL* 1.3 63.0 + - - +
691A ILE* 3.3 8.9 + - - +
692A TYR* 2.9 27.0 + - - +
732A ASP* 5.6 1.1 - - - -
754A PHE* 5.5 5.5 - - - -
942A GLY* 2.9 19.6 + - - -
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Residues in contact with VAL 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A LEU* 3.7 33.2 - - + -
683A THR* 3.5 33.4 - - + +
687A SER* 3.2 1.5 - - - +
688A SER* 1.3 74.6 - - - +
690A ASP* 1.3 59.4 + - - +
692A TYR* 3.1 5.6 + - - +
693A PHE* 2.9 61.1 + - + -
706A MET* 4.4 0.2 - - + -
730A ILE* 3.7 20.9 - - + +
731A TRP* 3.8 18.4 - - + -
732A ASP* 5.2 0.2 - - - +
942A GLY* 6.4 0.2 - - - -
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Residues in contact with ASP 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A THR* 5.2 3.0 - - + +
683A THR* 4.4 6.6 - - + +
684A VAL 4.2 3.1 - - - +
686A GLN* 3.7 22.6 + - - +
687A SER* 3.1 25.7 + - - +
689A VAL* 1.3 80.0 - - - +
691A ILE* 1.3 56.6 + - + +
693A PHE* 3.5 2.2 + - - +
694A ARG* 2.9 33.8 + - - +
703A TYR* 3.1 33.0 + - - -
706A MET* 5.2 1.1 - - - +
707A GLU* 5.6 0.3 - - - +
710A ASN* 3.9 16.9 + - - -
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Residues in contact with ILE 691 (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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485A GLY 4.0 2.2 - - - +
486A THR* 3.7 25.4 - - + -
487A GLN 5.4 0.7 - - - +
498A TRP* 4.8 2.5 - - + -
520A ASN* 3.7 13.0 - - - +
522A GLU* 3.6 41.7 - - + +
523A ARG* 3.6 31.9 - - + +
687A SER 3.0 13.1 + - - +
688A SER* 3.5 7.4 - - - +
689A VAL 3.3 0.2 - - - -
690A ASP* 1.3 76.0 - - - +
692A TYR* 1.3 64.2 + - - +
694A ARG* 3.2 30.3 + - - +
695A ARG* 3.3 15.3 + - + +
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Residues in contact with TYR 692 (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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538A LEU* 4.7 6.5 - - + -
667A ILE* 4.6 7.9 - - + +
688A SER 2.9 13.7 + - - +
689A VAL* 3.1 10.5 + - - +
691A ILE* 1.3 80.3 - - - +
693A PHE* 1.3 91.3 + + - +
694A ARG 3.4 0.2 + - - -
695A ARG 4.1 3.6 + - - +
696A GLN* 3.6 38.4 + - - +
699A LEU* 4.7 9.2 - - + +
753A PHE* 4.2 28.1 - + - +
754A PHE* 3.4 40.8 + + + +
784D PHE 4.3 2.5 - - - -
785D GLY* 3.7 23.3 - - - +
787D GLY* 4.9 9.3 - - - -
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Residues in contact with PHE 693 (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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667A ILE* 4.2 20.4 - - + -
672A LEU* 6.4 0.4 - - + -
681A TYR* 5.6 1.1 - + - -
689A VAL* 2.9 44.8 + - + +
692A TYR* 1.3 93.0 - + - +
694A ARG* 1.3 65.9 + - - +
696A GLN 4.4 0.7 - - - +
699A LEU* 3.3 44.3 - - + +
700A SER* 5.0 0.3 - - - -
702A MET* 3.5 40.6 - - + -
703A TYR* 3.4 19.8 - - + +
706A MET* 3.4 34.3 - - + -
730A ILE* 4.2 17.3 - - + -
753A PHE* 4.6 1.6 - + - -
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Residues in contact with ARG 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A THR* 5.6 2.2 - - - -
487A GLN* 3.5 33.3 + - - +
498A TRP* 6.3 0.6 - - - -
522A GLU* 4.1 15.2 - - - +
690A ASP* 2.9 21.5 + - - +
691A ILE* 3.5 32.2 + - - +
692A TYR 3.2 0.6 - - - -
693A PHE* 1.3 80.8 - - - +
695A ARG* 1.3 70.7 + - - +
696A GLN 2.9 12.3 + - - +
700A SER* 5.9 0.5 - - - -
703A TYR* 3.6 30.4 - - + +
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Residues in contact with ARG 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A GLU* 4.3 16.4 - - + +
691A ILE 3.3 10.9 + - - +
692A TYR 4.3 3.6 - - - +
694A ARG* 1.3 86.4 - - - +
696A GLN* 1.3 63.1 + - - +
785D GLY 5.1 4.9 - - - +
786D ASP* 6.0 0.5 - - - -
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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