Contacts of the strand formed by residues 714 - 722 (chain A) in PDB entry 1L8A
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 TYR 714 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662A TYR* 4.1 0.3 - - - -
664A TYR* 2.5 32.7 + + - -
665A GLU* 2.6 26.3 + - - -
702A PRO* 4.1 11.2 - - + -
705A ALA* 4.1 17.5 - - + +
708A GLY* 4.1 9.6 - - - -
709A ILE* 3.5 30.7 - - + -
713A ILE* 1.3 84.3 - - - +
715A LYS* 1.3 71.2 + - - +
716A LEU* 3.3 22.7 + - + +
756A TYR* 3.4 6.6 - - - -
757A SER* 3.1 43.7 + - - -
759A THR* 4.3 3.8 - - + -
791A VAL* 4.3 6.5 - - - -
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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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702A PRO* 5.4 3.1 - - - +
714A TYR* 1.3 78.9 - - - +
716A LEU* 1.3 65.8 + - - +
717A GLU* 4.0 11.9 - - - +
718A THR* 3.7 10.0 + - - +
754A ASP* 3.7 29.0 + - + +
755A VAL 3.6 7.4 - - - +
756A TYR* 3.3 44.2 + - + -
791A VAL* 4.3 12.3 + - + +
793A ASN* 4.2 4.0 + - - -
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Residues in contact with LEU 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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662A TYR* 3.8 14.8 - - + +
664A TYR* 3.7 22.2 - - - +
699A PRO* 6.0 0.9 - - + -
702A PRO* 4.2 16.4 - - + +
714A TYR* 3.3 20.2 + - + -
715A LYS* 1.3 74.4 - - - +
717A GLU* 1.3 66.1 + - + +
735A LEU* 4.2 12.1 - - + -
739A ARG* 3.0 51.4 - - + +
755A VAL* 2.5 22.4 + - + +
757A SER* 4.3 9.6 - - - +
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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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715A LYS* 3.4 7.2 - - - +
716A LEU* 1.3 84.5 - - - +
718A THR* 1.3 66.6 + - - +
719A ILE* 4.0 24.7 - - - +
739A ARG* 2.6 34.4 + - - +
754A ASP* 3.5 2.1 - - - -
755A VAL* 2.7 45.8 + - + +
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Residues in contact with THR 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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715A LYS* 3.7 10.4 + - - +
717A GLU* 1.3 82.0 - - - +
719A ILE* 1.3 72.3 + - - +
720A GLU* 4.2 16.9 + - - +
725A LYS* 3.5 18.2 - - - +
753A SER 3.2 4.0 - - - +
754A ASP* 2.7 25.4 + - - +
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Residues in contact with ILE 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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717A GLU* 4.0 22.9 - - + +
718A THR* 1.3 82.0 - - - +
720A GLU* 1.3 63.1 + - - +
725A LYS* 5.0 1.4 + - - +
739A ARG 5.1 1.6 - - - +
742A ALA* 3.5 39.0 - - + +
743A GLU* 4.3 16.8 - - + +
746A ALA* 3.5 29.8 - - + -
752A GLY* 3.0 4.4 - - - -
753A SER* 2.7 42.9 + - - +
755A VAL* 4.4 6.5 - - + -
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Residues in contact with GLU 720 (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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718A THR* 4.1 17.1 - - - +
719A ILE* 1.3 88.5 - - - +
721A GLY* 1.3 60.3 + - - +
746A ALA* 3.9 8.0 - - - +
752A GLY* 3.7 2.1 - - - -
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Residues in contact with GLY 721 (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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720A GLU* 1.3 80.5 + - - +
722A SER* 1.3 60.5 + - - -
724A GLY 3.3 15.2 - - - +
725A LYS* 5.6 0.3 - - - +
750A GLY* 2.9 22.9 - - - -
752A GLY* 3.3 13.4 + - - -
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Residues in contact with SER 722 (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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721A GLY* 1.3 72.4 - - - -
723A LYS* 1.3 71.0 + - - +
724A GLY 3.4 0.8 + - - -
750A GLY* 2.9 4.6 + - - -
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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