Contacts of the strand formed by residues 714 - 719 (chain A) in PDB entry 3L4U
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 GLN 714 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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694A TYR* 3.4 12.7 - - - -
695A VAL* 2.8 32.2 + - - +
710A ARG* 4.4 8.6 + - - +
711A TRP* 3.4 17.3 - - + +
712A ARG 2.9 36.4 + - - +
713A LYS* 1.3 75.9 - - - +
715A LYS* 1.3 67.2 + - - +
716A VAL* 3.8 12.5 - - + +
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Residues in contact with LYS 715 (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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668A VAL* 6.5 0.7 - - - -
692A MET* 4.4 20.5 + - + +
693A ALA* 3.3 23.1 - - - +
694A TYR* 3.6 21.7 - - + +
714A GLN* 1.3 79.6 - - - +
716A VAL* 1.3 64.8 + - - +
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Residues in contact with VAL 716 (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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691A VAL 3.5 0.7 - - - +
692A MET* 3.4 8.0 - - - +
693A ALA* 2.7 37.9 + - + +
695A VAL* 3.7 20.2 - - + -
711A TRP* 3.5 58.3 - - + +
714A GLN* 3.8 15.9 - - + +
715A LYS* 1.3 82.4 - - - +
717A GLU* 1.3 59.6 + - - +
718A MET* 4.2 15.7 - - + +
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Residues in contact with GLU 717 (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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690A LYS* 3.5 24.4 + - + +
691A VAL 3.5 5.2 - - - +
692A MET* 3.7 23.8 - - + +
711A TRP* 4.8 6.4 - - - -
716A VAL* 1.3 74.6 - - - +
718A MET* 1.3 61.6 + - - +
719A GLU* 2.9 32.9 + - - +
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Residues in contact with MET 718 (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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671A GLN* 4.7 1.8 - - - +
679A LEU* 5.4 3.1 - - + -
681A THR* 3.8 29.6 - - - +
690A LYS* 3.1 4.2 - - - -
691A VAL* 2.7 51.6 + - + +
693A ALA* 3.8 20.4 - - + -
695A VAL* 4.5 9.2 - - + -
711A TRP* 4.0 29.4 - - + -
716A VAL* 3.6 10.2 + - + -
717A GLU* 1.3 72.7 - - - +
719A GLU* 1.3 63.3 + - - +
720A LEU* 3.5 15.5 + - + +
726A GLY* 4.4 4.0 - - - -
728A HIS* 3.8 30.1 - - + +
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Residues in contact with GLU 719 (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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689A GLU 3.9 4.6 - - - +
690A LYS* 3.6 23.0 - - - +
711A TRP* 5.5 2.0 - - - -
717A GLU* 2.9 31.2 + - - +
718A MET* 1.3 72.0 - - - +
720A LEU* 1.3 68.5 + - - +
721A PRO* 3.8 10.1 - - + +
724A LYS* 5.7 0.2 - - - +
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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