Contacts of the strand formed by residues 686 - 691 (chain A) in PDB entry 6CIM
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 GLU 686 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A GLU 3.8 0.5 - - - +
519A TRP* 3.5 6.0 - - - -
520A GLN* 2.9 39.7 + - + +
590A PRO* 5.1 7.9 - - - +
685A SER* 1.3 79.7 + - - +
687A LEU* 1.3 62.7 + - - +
688A THR* 3.8 3.4 + - + +
697A THR* 4.2 22.2 + - + +
698A PHE 3.7 6.5 + - - +
699A LYS* 3.4 41.4 + - + +
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Residues in contact with LEU 687 (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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517A PHE* 3.7 26.9 - - + -
518A GLU 3.6 8.1 - - - +
519A TRP* 3.4 46.5 - - + +
563A LEU* 5.7 0.2 - - + -
564A VAL* 4.0 16.4 - - + +
567A LEU* 4.1 15.9 - - + -
686A GLU* 1.3 70.8 - - - +
688A THR* 1.3 64.5 + - - +
689A LEU* 4.5 7.0 - - + -
696A ARG 3.5 0.7 - - - +
697A THR* 3.0 6.6 - - - -
698A PHE* 2.8 50.7 + - + +
700A PHE* 4.0 22.7 - - + -
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Residues in contact with THR 688 (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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517A PHE* 3.6 3.8 - - - +
518A GLU* 2.9 58.7 + - - +
520A GLN* 3.7 25.3 - - - +
686A GLU* 4.6 5.2 - - + +
687A LEU* 1.3 73.2 - - - +
689A LEU* 1.3 63.6 + - - +
695A PRO* 5.6 6.1 - - - -
696A ARG 3.1 6.7 - - - -
697A THR* 3.5 25.4 - - + -
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Residues in contact with LEU 689 (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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515A HIS* 4.4 5.2 - - + -
516A PRO* 3.2 28.5 - - + +
517A PHE* 4.3 1.8 - - + +
564A VAL* 3.9 33.0 - - + +
567A LEU* 4.4 14.4 - - + -
568A MET* 3.8 34.5 - - + -
687A LEU* 4.5 13.0 - - + -
688A THR* 1.3 75.5 - - - +
690A GLU* 1.3 68.8 + - - +
691A MET* 3.6 3.9 + - + -
695A PRO* 4.3 2.8 - - - +
696A ARG* 2.9 32.3 + - - +
698A PHE* 4.4 18.1 - - + -
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Residues in contact with GLU 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PRO* 4.7 5.8 + - + +
568A MET* 3.7 23.4 - - - +
689A LEU* 1.3 77.7 - - - +
691A MET* 1.3 62.0 + - - +
693A GLY* 3.3 40.5 - - - +
694A ILE 3.7 5.2 - - - +
695A PRO* 4.1 13.5 - - + +
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Residues in contact with MET 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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567A LEU 4.5 8.7 - - - +
568A MET* 3.8 21.5 - - - +
571A GLU* 3.2 35.7 - - + +
574A ILE* 4.1 37.2 - - + -
575A LEU* 4.2 12.6 - - + -
591A PHE* 5.7 1.8 - - + -
689A LEU* 3.6 3.3 + - + +
690A GLU* 1.3 71.4 - - - +
692A GLY* 1.3 65.8 + - - +
693A GLY 3.1 0.9 - - - -
694A ILE 2.9 21.8 + - - +
696A ARG* 3.1 29.1 + - + +
698A PHE* 3.8 30.1 - - + -
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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