Contacts of the strand formed by residues 173 - 182 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ASN* 3.1 8.9 + - - -
170A PHE 3.1 25.8 + - - +
171A GLN* 3.3 0.6 - - + -
172A ARG* 1.3 85.5 - - + +
174A CYS* 1.3 63.7 + - - +
175A TYR* 3.5 23.8 - - + +
200A SER* 2.9 20.8 + - - -
202A HIS* 4.1 6.1 - - + -
206A GLU* 2.8 25.8 + - - +
283A ASP* 2.8 38.5 + - - -
284A ARG 3.4 10.1 - - - +
285A LEU* 4.3 14.1 - - + -
286A ALA 3.9 0.2 - - - +
301A GOL 4.6 8.0 + - - +
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Residues in contact with CYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A THR 3.5 0.2 - - - -
163A CYS* 2.0 54.7 - - + -
164A PRO* 4.1 4.7 - - + -
167A TRP* 3.6 10.4 - - + -
168A ILE 3.5 4.9 - - - -
173A LYS* 1.3 72.1 - - - +
175A TYR* 1.3 64.0 + - - +
283A ASP* 3.0 8.3 - - - +
284A ARG* 2.7 44.1 + - + -
285A LEU 4.2 2.9 - - - -
286A ALA* 3.5 24.2 - - - -
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS 4.5 0.2 - - - +
167A TRP* 3.5 6.1 - - - -
168A ILE* 2.9 43.7 + - - +
170A PHE* 3.6 30.4 + - + -
171A GLN* 5.5 0.9 + - - +
173A LYS* 3.5 36.2 - - + +
174A CYS* 1.3 76.2 - - - +
176A TYR* 1.3 60.9 + - - +
177A PHE* 3.9 23.6 + - + -
199A VAL* 3.9 17.7 - - + -
206A GLU* 2.5 38.3 + - + +
209A PHE* 3.6 13.2 - + + -
210A LEU* 3.8 21.8 - - + -
281A VAL* 4.7 1.6 - - + -
282A CYS 3.2 6.7 - - - +
283A ASP* 3.9 10.3 - - + -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS* 3.7 52.4 + - + -
167A TRP* 3.6 33.1 - + + -
175A TYR* 1.3 72.1 - - - +
177A PHE* 1.3 64.9 + - - +
178A GLY* 3.5 28.2 + - - -
194A MET* 3.5 35.5 - - + -
280A TRP* 3.8 12.4 - + - +
281A VAL* 3.4 6.8 - - - +
282A CYS* 2.9 38.2 + - + -
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS 5.4 1.0 + - - -
168A ILE* 4.2 21.3 - - + -
175A TYR* 3.9 20.0 - - + -
176A TYR* 1.3 81.6 - - - +
178A GLY* 1.3 61.2 + - - +
179A LYS* 3.9 17.8 + - - +
209A PHE* 3.8 27.6 - + - -
210A LEU* 3.9 24.2 - - + -
213A HIS* 3.5 48.9 - - + +
214A ALA* 4.5 3.1 - - - -
215A SER 5.7 0.4 - - - -
262A MET* 5.7 0.2 - - + -
280A TRP 4.0 2.9 - - - -
281A VAL* 3.7 23.3 - - + -
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.5 25.1 + - - -
177A PHE* 1.3 76.8 - - - +
179A LYS* 1.3 61.9 + - - +
279A ALA* 3.3 9.5 - - - +
280A TRP* 2.9 50.4 + - - +
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Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PHE* 4.3 16.7 - - - +
178A GLY* 1.3 81.5 - - - +
180A GLY* 1.3 62.4 + - - +
182A LYS* 5.2 0.5 - - - -
213A HIS 5.0 4.8 + - - -
215A SER* 3.3 37.4 + - - +
278A GLY 3.4 10.5 - - - +
279A ALA* 4.5 2.4 - - + +
280A TRP* 3.7 12.4 - - - -
301D GOL 6.1 0.9 - - - -
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LYS* 1.3 75.6 - - - +
181A THR* 1.3 66.5 + - - -
182A LYS* 3.2 8.9 + - - +
277A LEU 3.5 4.5 - - - +
278A GLY* 2.9 12.7 + - - -
280A TRP* 3.0 22.8 + - - -
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLY* 1.3 68.1 - - - -
182A LYS* 1.3 67.2 + - - +
276A LYS* 3.5 42.3 + - + +
277A LEU 3.2 9.4 - - - +
278A GLY* 4.1 6.5 - - - -
193D ASP* 3.9 14.6 - - - +
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LYS 5.2 0.4 - - - -
180A GLY* 3.2 10.4 + - - +
181A THR* 1.3 80.7 + - - +
183A GLN* 1.3 67.1 + - - +
186A HIS* 3.4 32.6 + - + +
187A ALA* 4.0 14.6 - - + +
190A ALA* 4.1 2.5 - - - -
220A TRP* 2.8 19.2 + - - -
276A LYS* 4.2 4.9 - - - +
277A LEU 2.8 22.2 + - - +
280A TRP* 3.4 44.9 - - + +
193D ASP* 4.6 4.5 - - - -
301D GOL 2.8 43.5 + - - -
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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