Contacts of the strand formed by residues 771 - 775 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C MET* 3.6 12.3 - - + +
186C ILE* 4.9 8.7 - - + -
207C ILE* 4.3 6.1 - - + -
211C ASN* 4.1 3.6 - - - +
246C PHE* 3.5 38.1 - - + -
758C TYR* 3.4 10.4 - - - -
759C VAL* 3.1 35.5 + - + -
760C ASN* 2.7 31.3 + - - +
761C ASP 4.2 0.2 - - - -
762C PHE* 3.8 15.0 - - + -
770C LYS* 1.3 77.6 - - - +
772C TYR* 1.4 68.8 + - - +
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Residues in contact with TYR 772 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C ALA* 3.6 16.8 - - + -
184C MET 2.9 9.4 + - - +
185C ARG* 3.6 34.0 + - - +
186C ILE* 3.0 25.8 + - - +
273C GLU* 3.8 32.0 + - + +
755C GLY 6.0 0.2 - - - -
756C GLY* 4.9 3.8 - - - -
757C SER 3.4 20.9 - - - -
758C TYR* 3.7 24.8 - - + +
759C VAL 4.7 0.2 - - - +
770C LYS* 3.3 39.9 - - + +
771C VAL* 1.4 74.7 - - - +
773C VAL* 1.3 61.3 + - - +
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Residues in contact with VAL 773 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ILE* 3.4 27.8 - - + +
188C MET* 4.4 13.0 - - + -
203C VAL* 4.4 7.4 - - + -
204C ILE* 4.0 24.5 - - + -
207C ILE* 4.0 22.7 - - + -
752C ALA* 3.4 9.6 - - + +
756C GLY* 3.2 3.3 - - - -
757C SER* 3.0 39.6 + - - +
759C VAL* 4.1 8.2 - - + +
771C VAL* 5.4 0.2 - - + -
772C TYR* 1.3 76.4 - - - +
774C MET* 1.3 63.1 + - - +
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Residues in contact with MET 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLY* 5.9 0.9 - - - -
222B THR 4.0 13.5 - - - +
223B PRO* 5.3 0.4 - - - -
185C ARG* 3.5 26.7 - - - +
186C ILE 3.0 9.8 + - - +
187C TRP* 3.3 16.0 - - + -
188C MET* 2.9 29.5 + - - +
752C ALA 3.4 7.0 - - - -
753C ALA 3.6 7.4 - - - +
754C TRP 3.8 20.6 - - - +
755C GLY* 4.0 10.3 - - - +
756C GLY* 3.8 14.6 - - - +
773C VAL* 1.3 77.9 - - - +
775C SER* 1.3 70.5 + - - +
780C ARG* 3.7 27.6 - - - +
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Residues in contact with SER 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C TRP* 3.4 10.1 - - - -
188C MET* 3.5 12.5 + - - +
753C ALA* 3.0 27.5 + - - +
774C MET* 1.3 75.0 - - - +
776C GLU* 1.3 72.6 + - - +
779C TYR* 3.7 10.6 - - - +
780C ARG* 2.8 29.2 + - - -
789C TRP* 3.3 33.0 - - - -
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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