Contacts of the strand formed by residues 707 - 713 (chain A) in PDB entry 2LNX
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 PHE 707 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668A TYR* 5.0 9.0 - + - -
674A PHE* 3.5 20.2 - + - -
697A ILE* 4.7 7.2 - - + -
698A ARG 3.5 17.3 - - - +
699A GLU* 3.3 41.1 - - + +
705A GLU* 4.4 5.5 - - - +
706A ARG* 1.3 113.9 + - + +
708A ALA* 1.3 61.8 + - - +
722A VAL* 3.2 39.8 + - + +
724A GLU* 4.1 5.2 - - - -
729A ILE* 5.1 0.6 - - + +
740A LEU* 3.3 34.5 - - + -
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Residues in contact with ALA 708 (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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697A ILE* 3.1 8.2 - - - +
698A ARG* 2.9 50.0 + - + +
699A GLU* 5.4 0.2 - - - +
700A ARG* 5.7 6.0 - - + +
705A GLU* 5.9 3.1 - - + -
707A PHE* 1.3 75.3 - - - +
709A ILE* 1.3 66.3 + - - +
720A ILE 3.8 11.4 - - - +
721A LYS* 5.5 9.2 - - - +
722A VAL* 4.3 1.6 - - - -
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Residues in contact with ILE 709 (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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695A TYR* 5.7 2.5 - - + -
696A LEU 3.8 13.2 - - - +
697A ILE* 4.2 20.2 - - + +
698A ARG* 5.5 1.1 - - - -
708A ALA* 1.3 82.6 - - - +
710A SER* 1.3 75.9 + - - +
711A ILE* 4.8 5.2 - - + +
719A HIS* 3.3 3.1 + - - +
720A ILE* 2.8 49.2 + - + +
722A VAL* 3.5 25.8 - - + -
731A ILE* 4.0 15.3 - - + -
740A LEU* 6.1 1.3 - - + -
743A LEU* 5.3 3.4 - - + -
744A VAL* 5.3 8.5 - - + -
747A TYR* 3.9 30.3 - - + +
763A LEU* 6.0 0.2 - - + -
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Residues in contact with SER 710 (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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683A THR* 3.1 29.8 - - - +
687A LEU* 3.6 8.5 - - - +
695A TYR* 4.0 0.3 - - - -
696A LEU* 3.0 42.9 + - - +
698A ARG* 4.0 6.7 + - - -
709A ILE* 1.3 76.4 + - - +
711A ILE* 1.3 61.1 + - - +
717A VAL* 4.7 0.2 - - - -
718A LYS 3.3 8.3 - - - -
719A HIS* 2.9 29.2 + - - -
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Residues in contact with ILE 711 (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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687A LEU* 4.0 3.1 - - - -
693A GLY* 5.6 2.0 - - - -
694A THR 3.2 20.0 - - - +
695A TYR* 3.8 19.1 - - + -
709A ILE* 4.3 6.0 - - + +
710A SER* 1.3 74.7 - - - +
712A LYS* 1.3 76.3 + - - +
713A PHE 5.1 0.2 - - - +
717A VAL* 3.5 3.5 - - - +
718A LYS* 2.8 39.6 + - + +
720A ILE* 5.6 6.8 - - + +
747A TYR* 5.5 1.3 - - + +
752A LEU* 5.1 5.4 - - + -
759A LEU* 3.9 29.4 - - + -
761A THR* 4.3 20.4 - - + +
762A THR 4.6 10.5 - - - +
763A LEU* 3.8 16.2 - - + -
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Residues in contact with LYS 712 (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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687A LEU* 3.4 41.5 + - + +
688A LYS 5.2 3.3 + - - -
689A SER 5.2 0.6 - - - -
690A HIS 2.8 25.8 + - - +
691A ALA* 3.1 29.6 - - - +
692A SER* 3.5 2.6 + - - +
693A GLY* 3.1 21.7 + - - -
694A THR* 2.9 14.7 + - - +
711A ILE* 1.3 79.1 - - - +
713A PHE* 1.3 64.4 + - - +
715A ASP* 3.5 44.4 + - - +
716A GLU 3.3 17.3 - - - +
717A VAL* 4.1 0.9 - - + -
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Residues in contact with PHE 713 (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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692A SER* 3.5 35.7 - - - +
711A ILE* 4.3 2.1 - - + +
712A LYS* 1.3 76.0 - - - +
714A ASN* 1.3 84.4 + - + +
715A ASP 3.2 1.8 - - - -
716A GLU* 2.9 23.5 + - - +
718A LYS* 5.1 4.3 + - + +
758A GLN 5.3 3.1 - - - -
759A LEU* 3.5 34.8 - - + -
760A ASP* 3.6 25.6 - - - -
761A THR* 3.5 35.9 - - + -
764A LYS* 5.7 2.7 - - - -
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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