Contacts of the strand formed by residues 707 - 713 (chain A) in PDB entry 5HLB
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 ASP 707 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A ARG* 2.8 52.0 + - - -
507A SER* 4.0 6.9 + - - +
701A THR* 3.3 7.3 - - - +
702A THR* 2.8 58.5 + - + +
705A ASN 4.8 0.6 - - - -
706A VAL* 1.3 87.4 + - - +
708A THR* 1.3 65.9 + - - +
709A TRP* 3.9 10.5 - - - +
722A TRP* 3.3 11.7 + - - +
723A VAL 3.5 6.1 - - - -
731A THR* 5.3 0.7 - - - -
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Residues in contact with THR 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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700A GLY 3.2 6.3 - - - -
701A THR* 4.2 4.7 - - + -
707A ASP* 1.3 78.3 - - - +
709A TRP* 1.3 62.3 + - - +
722A TRP* 3.5 4.5 - - - -
723A VAL* 2.9 46.6 + - - +
731A THR* 4.7 3.8 - - - +
733A LEU* 3.4 40.8 - - + +
736A ALA* 3.9 20.6 - - - -
738A GLY* 3.7 3.5 - - - +
739A ALA* 3.2 23.9 + - - +
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Residues in contact with TRP 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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506A ARG* 3.7 26.0 - - + -
507A SER 3.0 19.4 + - - -
508A ILE* 3.3 25.7 - - + +
511A LEU* 3.6 32.8 - - + -
616A LEU 4.1 9.0 - - - -
618A PRO* 4.1 13.7 - - + -
621A VAL* 4.0 18.6 - - + -
699A THR 3.7 0.5 - - - -
700A GLY* 2.8 35.0 + - - -
702A THR* 4.9 1.8 - - + -
707A ASP* 3.9 14.5 - - + +
708A THR* 1.3 77.2 - - - +
710A PHE* 1.3 60.5 + - - +
720A ILE* 3.8 21.5 - - + -
721A THR 3.4 11.7 - - - -
722A TRP* 3.6 41.1 - + + -
736A ALA* 3.1 13.3 - - - +
739A ALA* 3.7 3.6 - - - -
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Residues in contact with PHE 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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511A LEU* 4.8 3.6 - - - -
677A VAL* 5.5 0.4 - - + -
678A VAL* 4.2 14.4 - - + -
683A GLY* 4.6 5.4 - - - -
686A LEU* 4.5 7.2 - - + -
695A LEU* 6.4 0.7 - - + -
697A GLY* 4.1 7.0 - - - -
698A LYS* 3.3 26.5 - - - -
699A THR* 3.6 26.0 - - + -
709A TRP* 1.3 75.4 - - - +
711A ALA* 1.3 72.7 + - - +
712A GLY* 3.9 3.1 - - - -
719A THR 3.4 4.0 - - - +
720A ILE* 3.5 2.8 - - - +
721A THR* 2.8 40.1 + - - +
736A ALA* 4.5 0.2 - - + -
739A ALA* 4.2 22.2 - - + +
740A MET* 3.7 26.7 - - + +
743A TYR* 3.6 37.6 - + + -
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Residues in contact with ALA 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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511A LEU* 4.5 5.4 - - + +
625A PHE* 3.9 36.8 - - + -
674A MET* 4.8 1.3 - - + +
696A ALA 3.9 0.2 - - - +
697A GLY* 3.0 25.3 - - - -
698A LYS 3.1 15.7 + - - +
710A PHE* 1.3 74.4 - - - +
712A GLY* 1.3 59.0 + - - +
713A ILE* 5.3 2.7 - - + -
719A THR 3.5 4.9 - - - -
720A ILE* 3.7 20.9 - - + -
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Residues in contact with GLY 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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695A LEU* 5.8 1.3 - - - -
696A ALA 3.8 2.2 - - - -
710A PHE* 3.9 10.7 - - - -
711A ALA* 1.3 74.1 - - - +
713A ILE* 1.3 61.8 + - - -
714A ASP* 4.3 0.3 + - - +
717A THR* 3.8 1.4 + - - +
718A VAL* 3.6 3.0 - - - +
719A THR* 2.8 45.0 + - - +
720A ILE* 5.0 0.2 - - - +
743A TYR* 3.7 25.8 + - - -
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Residues in contact with ILE 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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479A ARG* 4.4 8.5 - - - +
625A PHE* 4.5 13.7 - - + +
628A ILE* 5.2 0.7 - - + -
629A ALA* 3.8 31.2 - - + +
671A LEU* 3.8 25.4 - - + -
674A MET* 3.8 23.1 - - + -
695A LEU* 3.5 11.8 - - - +
696A ALA* 2.7 36.3 + - + +
711A ALA 5.3 0.7 - - - +
712A GLY* 1.3 77.5 - - - +
714A ASP* 1.3 72.1 + - - +
717A THR 3.5 6.7 - - - +
718A VAL* 4.3 12.8 - - + -
743A TYR* 4.1 1.0 + - - -
755A LEU* 3.5 14.5 - - + +
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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