Contacts of the strand formed by residues 173 - 182 (chain C) in PDB entry 4GJ0
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 LYS 173 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C ASN* 3.0 21.1 + - - -
170C PHE 3.1 14.2 + - - +
171C GLN* 3.3 0.4 - - - +
172C ARG* 1.3 87.7 - - + +
174C CYS* 1.3 64.1 + - - +
175C TYR* 3.4 24.9 - - + +
200C SER* 3.1 13.3 + - - -
202C HIS* 5.3 4.0 - - - -
206C GLU* 2.8 26.9 + - - +
283C ASP* 2.9 35.4 + - - -
284C ARG 3.4 11.0 - - - +
285C LEU* 4.2 14.1 - - + -
286C ALA 4.0 0.2 - - - +
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Residues in contact with CYS 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C THR 3.5 8.5 - - - -
163C CYS* 2.0 54.5 - - + -
164C PRO* 4.2 3.4 - - + -
167C TRP* 3.5 17.2 - - + -
168C ILE 3.4 4.5 - - - -
173C LYS* 1.3 72.3 - - - +
175C TYR* 1.3 62.6 + - - +
283C ASP* 3.0 8.1 - - - +
284C ARG* 2.7 37.8 + - + -
285C LEU 4.0 3.6 - - - -
286C ALA* 3.6 17.5 - - - -
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Residues in contact with TYR 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LYS 4.5 0.2 - - - +
167C TRP* 3.4 8.2 - - - -
168C ILE* 2.8 50.2 + - - +
170C PHE* 3.9 23.0 + + + -
171C GLN* 5.5 0.9 + - - -
173C LYS* 3.4 36.5 - - + +
174C CYS* 1.3 74.3 - - - +
176C TYR* 1.3 57.6 + - - +
177C PHE* 3.9 21.8 + - + -
199C VAL* 4.0 15.7 - - + -
206C GLU* 2.6 39.0 + - + +
209C PHE* 3.5 15.5 - + + -
210C LEU* 3.7 22.9 - - + -
281C VAL* 4.7 1.1 - - + -
282C CYS 3.2 6.5 - - - +
283C ASP* 3.9 13.9 - - + -
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Residues in contact with TYR 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LYS* 3.7 53.6 + - + -
167C TRP* 3.5 38.5 - + + -
175C TYR* 1.3 74.3 - - - +
177C PHE* 1.3 64.8 + - - +
178C GLY* 3.5 28.8 + - - -
179C LYS 5.7 0.2 + - - -
194C MET* 3.4 32.4 - - + -
280C TRP* 3.7 12.3 - + - +
281C VAL* 3.3 7.0 - - - +
282C CYS* 2.8 35.7 + - + -
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Residues in contact with PHE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LYS 5.3 1.6 + - - -
168C ILE* 4.1 20.4 - - + -
175C TYR* 3.9 20.9 - - + -
176C TYR* 1.3 78.9 - - - +
178C GLY* 1.3 64.5 + - - +
179C LYS* 3.9 23.3 + - - +
209C PHE* 4.0 10.5 - + - -
210C LEU* 3.9 28.9 - - + -
213C HIS* 3.4 52.7 - + + +
214C ALA* 4.3 3.4 - - - -
215C SER 5.7 0.7 - - - -
262C MET* 5.7 0.2 - - + -
280C TRP 3.9 2.2 - - - -
281C VAL* 3.8 29.2 - - + -
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Residues in contact with GLY 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C TYR* 3.5 23.8 + - - -
177C PHE* 1.3 75.6 - - - +
179C LYS* 1.3 68.7 + - - +
279C ALA* 3.3 5.2 - - - +
280C TRP* 2.8 50.3 + - - +
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Residues in contact with LYS 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C TYR* 5.7 0.4 + - - -
177C PHE* 3.9 25.7 + - - +
178C GLY* 1.3 86.1 + - - +
180C GLY* 1.3 60.8 + - - +
182C LYS* 4.8 1.6 - - - -
213C HIS 4.5 8.5 + - - -
214C ALA 5.2 0.2 - - - -
215C SER* 4.3 27.4 - - - +
278C GLY 3.4 9.9 - - - +
279C ALA* 4.6 1.7 - - - +
280C TRP* 3.8 13.0 + - - -
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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
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179C LYS* 1.3 75.4 - - - +
181C THR* 1.3 66.1 + - - -
182C LYS* 3.3 9.6 + - - +
277C LEU 3.3 8.3 - - - +
278C GLY* 3.0 13.6 + - - +
280C TRP* 3.3 17.8 + - - -
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Residues in contact with THR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ASP* 4.2 20.8 + - - +
180C GLY* 1.3 70.7 - - - -
182C LYS* 1.3 64.6 + - - +
186C HIS* 4.3 2.8 + - - -
276C LYS* 4.6 21.3 + - + +
277C LEU 3.2 8.1 - - - -
278C GLY* 4.3 11.7 - - - +
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Residues in contact with LYS 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ASP* 3.5 5.8 - - - -
179C LYS 4.8 3.8 - - - -
180C GLY* 3.3 10.0 + - - +
181C THR* 1.3 81.2 + - - +
183C GLN* 1.3 66.4 + - - +
186C HIS* 3.4 23.2 + - + +
187C ALA* 3.9 17.0 - - + +
190C ALA* 4.0 2.5 - - + -
220C TRP* 2.9 20.8 + - - -
276C LYS* 4.0 2.4 - - - +
277C LEU 2.9 20.3 + - - +
280C TRP* 3.4 44.0 - - + +
301C GOL 3.0 50.3 + - - -
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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
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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