Contacts of the strand formed by residues 178 - 183 (chain C) in PDB entry 6DKS
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 178 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LYS* 5.9 1.2 - - - +
171C MET 3.4 15.1 + - - +
172C PHE* 3.8 11.7 - - + +
173C TYR* 5.5 0.8 - - - -
176C SER 3.2 7.2 + - - +
177C ASP* 1.3 70.2 - - - +
179C ILE* 1.4 61.1 + - - +
180C GLY* 3.6 10.8 + - - -
181C VAL* 5.8 1.4 - - - +
374C LEU 5.1 3.3 - - - +
375C ALA 5.0 1.2 - - - -
376C PRO* 3.4 40.0 - - + +
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Residues in contact with ILE 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TRP* 4.0 17.3 - - + -
125C PRO* 4.4 1.1 - - + -
171C MET* 3.0 24.4 + - + +
172C PHE* 3.8 24.9 - - - +
173C TYR* 3.5 47.3 - - + +
177C ASP 3.6 0.4 + - - -
178C ASP* 1.4 70.9 - - - +
180C GLY* 1.3 58.3 + - - +
182C PHE* 3.7 27.4 - - + -
366C PHE* 4.0 18.8 - - + -
376C PRO* 3.3 2.6 - - - +
377C VAL* 3.0 38.2 + - + +
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Residues in contact with GLY 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C VAL 3.6 1.2 - - - +
170C LYS* 3.6 1.2 - - - -
171C MET* 2.8 35.9 + - - +
178C ASP* 3.6 8.8 + - - +
179C ILE* 1.3 79.8 - - - +
181C VAL* 1.3 62.7 + - - -
182C PHE* 3.9 2.5 - - - -
376C PRO* 4.0 7.9 - - - -
378C THR* 3.1 17.7 - - - -
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C SER* 3.4 25.4 - - - +
169C VAL 3.4 5.8 - - - +
170C LYS* 4.4 15.9 - - + -
178C ASP* 5.8 1.1 - - - +
180C GLY* 1.3 76.3 - - - +
182C PHE* 1.3 63.6 + - - +
183C LEU* 4.1 15.8 + - + +
378C THR* 2.9 25.1 + - - +
379C PRO* 5.0 3.5 - - - +
380C VAL 5.6 0.2 + - - -
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Residues in contact with PHE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL* 3.8 26.0 - - + -
76C ILE* 3.4 23.2 - - + +
167C LEU 3.8 0.3 - - - +
169C VAL* 2.8 40.2 + - + +
171C MET* 4.2 11.0 - - + -
179C ILE* 3.7 23.1 - - + -
180C GLY 3.9 8.5 - - - -
181C VAL* 1.3 74.6 - - - +
183C LEU* 1.3 62.3 + - - +
364C TYR* 3.5 44.2 - + + -
366C PHE* 3.6 25.1 - + - -
377C VAL* 4.4 0.4 - - + -
378C THR* 3.5 27.4 - - + -
380C VAL* 3.7 8.7 - - + -
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Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 3.6 2.4 - - - +
166C MET* 4.2 32.1 - - + +
167C LEU 3.2 12.1 - - - +
168C SER* 3.7 26.0 - - - +
181C VAL* 4.1 12.8 - - + +
182C PHE* 1.3 74.6 - - - +
184C SER* 1.3 67.2 + - - +
362C ALA* 3.6 1.7 - - - +
364C TYR* 2.6 39.2 + - - +
403C ASN* 5.6 8.3 - - - +
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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
------------------------------------------------------------
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