Contacts of the strand formed by residues 699 - 702 (chain A) in PDB entry 3I7L
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 LEU 699 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A SER* 3.3 26.7 - - - -
402A ILE* 2.9 36.8 + - + +
404A LEU* 4.1 21.8 - - + -
407A ILE* 4.0 12.1 - - + -
410A LEU* 4.7 15.3 - - + -
425A LEU* 6.4 0.7 - - + -
427A LEU* 4.7 7.4 - - + -
436A LEU* 4.9 12.3 - - + -
692A ALA* 5.1 4.9 - - + -
693A LEU 3.6 15.9 - - - +
694A ALA* 5.1 0.2 - - - -
695A ASN* 3.4 4.3 - - - -
698A THR* 1.3 79.7 - - - +
700A THR* 1.3 88.1 + - - +
701A ILE* 4.3 7.4 - - + -
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Residues in contact with THR 700 (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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396A ILE* 5.0 6.1 - - + -
398A GLU* 3.7 35.0 + - + +
401A SER* 3.2 26.5 - - - +
693A LEU* 2.7 45.1 + - - +
695A ASN* 3.0 17.3 + - - -
698A THR* 4.7 1.8 - - + +
699A LEU* 1.3 84.0 + - - +
701A ILE* 1.3 75.3 + - - +
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Residues in contact with ILE 701 (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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396A ILE* 5.8 1.8 - - - -
397A HIS 3.8 0.3 - - - +
398A GLU* 4.3 1.5 - - - -
399A HIS* 3.4 28.5 + - - -
400A ALA 3.7 20.6 + - - +
402A ILE* 4.4 11.0 - - + -
438A LEU* 6.0 3.4 - - + -
682A LEU* 4.0 21.3 - - + -
687A TYR* 4.2 32.1 - - + -
690A SER* 4.2 4.7 - - - +
691A LEU 3.4 13.9 - - - +
692A ALA* 3.8 12.6 - - + -
693A LEU* 5.4 0.7 - - - -
699A LEU* 4.3 13.9 - - + -
700A THR* 1.3 91.7 - - - +
702A GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 702 (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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396A ILE* 5.3 5.3 - - - +
397A HIS 3.2 18.6 - - - -
399A HIS* 3.9 9.9 - - - -
690A SER* 2.9 24.1 + - - -
691A LEU* 3.2 19.4 + - - +
693A LEU* 5.5 1.9 - - - +
701A ILE* 1.3 72.9 - - - +
703A THR* 1.3 65.7 + - - +
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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