Contacts of the strand formed by residues 771 - 775 (chain A) in PDB entry 5NC5
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 VAL 771 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A MET* 3.5 16.4 - - + +
186A ILE* 4.6 9.6 - - + -
207A ILE* 4.7 4.7 - - + -
246A PHE* 4.0 24.0 - - + -
758A TYR* 3.4 8.8 - - - -
759A VAL* 3.0 32.2 + - + -
760A ASN* 2.8 36.9 + - - +
761A ASP 3.8 13.2 - - - -
762A PHE* 3.9 14.8 - - + -
770A LYS* 1.3 77.4 - - - +
772A TYR* 1.3 68.4 + - - +
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Residues in contact with TYR 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PRO* 5.5 7.1 - - + +
125A GLN* 3.0 28.3 + - - -
183A ALA* 4.1 13.2 - - + -
184A MET 3.1 8.1 + - - +
185A ARG* 3.5 33.1 + - - +
186A ILE* 3.0 29.3 + - - +
273A GLU* 4.1 27.9 + - + +
756A GLY* 4.9 3.1 - - - -
757A SER* 3.3 25.8 - - - -
758A TYR* 3.6 20.2 - + + -
770A LYS* 3.7 29.3 - - + +
771A VAL* 1.3 77.5 - - - +
773A VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 4.4 0.3 + - - -
186A ILE* 3.6 23.1 - - + -
188A MET* 4.7 10.5 - - + -
203A VAL* 4.4 3.8 - - + -
204A ILE* 3.9 24.2 - - + -
207A ILE* 4.1 16.6 - - + -
752A ALA* 3.6 8.2 - - + +
756A GLY* 3.4 1.6 - - - -
757A SER* 3.0 45.6 + - - +
759A VAL* 3.5 19.1 - - + -
771A VAL* 5.6 0.2 - - + -
772A TYR* 1.3 74.1 - - - +
774A MET* 1.3 69.8 + - - +
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Residues in contact with MET 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 3.6 24.2 - - - +
186A ILE 3.0 9.5 + - - +
187A TRP* 3.2 11.1 - - + -
188A MET* 2.6 39.2 + - - +
752A ALA 3.4 10.5 - - - +
753A ALA 3.5 7.0 - - - +
754A TRP 4.0 9.2 - - - +
755A GLY* 3.9 18.6 - - - +
756A GLY* 3.7 12.6 - - - +
773A VAL* 1.3 81.6 - - - +
775A SER* 1.3 67.8 + - - +
780A ARG* 3.5 32.8 - - - +
221C GLY* 6.0 1.1 - - - -
222C THR 4.4 10.8 - - - +
223C PRO* 5.8 0.4 - - - -
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Residues in contact with SER 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TRP* 3.5 8.1 - - - -
188A MET* 3.6 10.8 + - - +
753A ALA* 3.1 22.2 + - - +
774A MET* 1.3 80.5 - - - +
776A GLU* 1.3 79.7 + - - +
779A TYR* 3.5 21.3 - - - +
780A ARG* 2.8 30.3 + - - +
789A TRP* 3.5 24.1 - - - -
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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
------------------------------------------------------------
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