Contacts of the strand formed by residues 689 - 696 (chain F) in PDB entry 5JLH
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 ASN 689 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184F SER* 4.8 7.1 + - - -
188F ASP* 5.2 6.3 + - - +
190F GLU* 5.3 7.1 + - - +
191F ASP 3.1 5.6 + - - +
192F GLN* 2.7 48.0 + - - +
193F SER 2.9 17.9 + - - +
509F THR* 4.4 8.1 - - - +
688F THR* 1.3 73.4 - - - +
690F PRO* 1.3 77.4 - - - +
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Residues in contact with PRO 690 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU* 5.4 1.9 - - - +
192F GLN* 4.9 0.6 - - - +
193F SER* 3.2 16.8 - - - +
195F LEU* 4.7 5.2 - - + -
505F LEU* 4.3 22.7 - - + -
509F THR* 3.3 35.3 - - + +
685F LEU 4.9 3.4 - - - +
688F THR 3.4 11.4 - - - +
689F ASN* 1.3 103.1 - - - +
691F SER* 1.3 62.5 + - - +
692F PHE* 3.6 19.8 - - + -
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Residues in contact with SER 691 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F LEU* 5.4 4.3 - - - +
177F VAL* 4.1 25.2 + - - +
181F ALA* 5.2 6.3 - - - -
192F GLN* 5.6 1.6 - - - -
193F SER 2.6 13.1 + - - -
194F ILE* 3.4 20.2 - - - +
195F LEU* 2.6 33.4 + - - +
689F ASN 5.2 0.4 - - - -
690F PRO* 1.3 75.9 - - - +
692F PHE* 1.3 68.6 + - - +
693F VAL* 5.5 0.3 - - - +
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Residues in contact with PHE 692 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU* 3.6 29.8 + - + +
141F PHE* 3.9 15.5 - - + -
142F CYS* 3.2 21.7 + - - +
177F VAL* 5.1 1.7 - - - +
195F LEU* 3.6 27.6 - - + -
505F LEU 5.4 0.2 - - - -
506F PHE* 3.1 52.9 - + + -
509F THR* 3.7 29.6 - - + -
690F PRO* 3.6 28.9 - - + -
691F SER* 1.3 87.7 + - - +
693F VAL* 1.3 66.2 + - - +
694F ARG* 3.7 13.0 - - - +
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Residues in contact with VAL 693 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F CYS* 3.4 18.8 - - + +
144F VAL* 4.1 20.2 - - + -
174F VAL* 5.3 12.3 - - + -
177F VAL* 4.2 22.9 - - + -
194F ILE* 4.2 22.0 - - + -
195F LEU 2.8 18.4 + - - +
196F CYS* 3.6 13.2 - - - +
197F THR 3.4 12.0 + - - -
207F ASN* 5.6 2.5 - - - +
691F SER* 5.5 0.4 - - - +
692F PHE* 1.3 79.7 - - - +
694F ARG* 1.3 75.0 + - - +
695F CYS* 4.2 9.1 + - - -
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Residues in contact with ARG 694 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F PHE* 3.1 47.1 - - + -
142F CYS 2.8 11.1 + - - +
143F VAL* 3.4 8.6 - - + -
144F VAL* 2.8 33.0 + - - +
195F LEU* 3.7 18.8 + - - +
197F THR* 3.1 40.3 - - - +
502F LEU* 5.6 3.4 + - - +
503F GLN* 4.0 13.3 + - - +
506F PHE* 4.5 12.9 - - - +
692F PHE* 3.7 20.2 - - - +
693F VAL* 1.3 81.9 + - - +
695F CYS* 1.3 59.8 + - - +
696F ILE* 3.9 3.5 - - + +
719F ASN* 3.0 41.5 + - - +
721F VAL* 4.0 9.4 - - + -
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Residues in contact with CYS 695 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F VAL* 3.4 21.1 - - + -
196F CYS* 4.7 5.6 - - - -
197F THR* 4.0 11.9 + - - +
198F GLY 4.9 0.5 - - - +
199F GLU* 3.3 36.3 - - + +
202F ALA* 4.6 5.4 - - + -
204F LYS* 3.8 30.7 - - + -
207F ASN* 5.7 2.5 - - - -
693F VAL* 4.2 13.5 - - - -
694F ARG* 1.3 77.9 - - - +
696F ILE* 1.3 66.7 + - - +
715F GLN* 5.1 0.7 - - - +
719F ASN* 5.3 2.6 + - - +
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Residues in contact with ILE 696 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F LEU* 5.6 1.1 - - + -
143F VAL* 3.7 29.6 - - + -
144F VAL 3.0 5.9 + - - -
145F ILE* 3.4 23.7 - - + +
146F ASN* 3.2 24.6 + - - +
199F GLU* 3.4 2.7 - - - -
202F ALA* 5.8 0.4 - - - -
694F ARG* 3.9 4.9 - - + +
695F CYS* 1.3 81.7 - - - +
697F VAL* 1.3 71.8 + - - +
712F VAL* 4.0 25.6 - - + -
715F GLN* 3.0 33.7 - - + +
716F LEU* 4.6 10.5 - - + -
719F ASN* 4.0 19.7 - - - +
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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