Contacts of the strand formed by residues 167 - 178 (chain C) in PDB entry 4RQZ
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 THR 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A SER* 3.7 9.6 - - - +
178A ARG* 3.1 22.0 + - - -
191A GLN* 3.1 24.5 + - - +
231A GLY 5.6 0.9 - - - +
232A ILE* 5.5 1.6 - - + -
157C ALA 3.3 5.9 - - - +
158C ILE* 3.6 1.9 - - - -
159C GLY 2.8 29.3 + - - -
161C PRO* 3.3 29.9 - - + +
164C LEU* 4.9 0.9 - - - +
165C GLY 3.2 4.9 + - - -
166C GLN* 1.3 73.3 - - - +
168C ILE* 1.3 65.5 + - - +
169C THR* 3.9 22.0 - - + -
200C ASN* 5.0 2.0 + - - +
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Residues in contact with ILE 168 (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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151A ILE* 3.4 29.6 - - + -
172A ILE* 3.6 21.6 - - + +
174A SER* 2.6 42.4 + - - +
51C VAL* 4.2 18.6 - - + -
55C ALA* 4.5 5.2 - - + -
156C LEU* 4.0 30.5 - - + -
157C ALA 3.5 2.9 - - - +
158C ILE* 3.7 38.6 - - + -
166C GLN* 4.6 6.7 - - + +
167C THR* 1.3 75.7 - - - +
169C THR* 1.3 60.9 + - - +
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Residues in contact with THR 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 4.1 3.1 - - - -
174A SER* 4.1 0.9 - - - +
193A ASP* 3.6 25.1 - - + -
230A GLU 5.7 0.4 - - - +
231A GLY 4.3 7.0 - - - +
232A ILE* 6.3 0.7 - - + -
156C LEU* 3.1 7.3 - - - +
157C ALA* 2.9 45.2 + - - +
161C PRO* 6.0 0.7 - - + -
167C THR* 3.9 17.0 - - + -
168C ILE* 1.3 80.2 - - - +
170C GLN* 1.3 61.5 + - - +
194C ALA* 4.0 0.8 - - - +
195C SER* 2.7 39.7 + - - +
197C ASN* 5.9 1.3 - - - +
200C ASN* 5.3 1.5 + - - +
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Residues in contact with GLN 170 (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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170A GLN* 3.1 32.2 + - - +
171A GLY* 4.7 1.7 - - - -
172A ILE* 3.8 19.1 - - + +
193A ASP* 2.9 17.0 + - - +
47B TYR* 6.0 0.4 - - - -
170B GLN* 3.1 21.1 + - - +
47C TYR* 4.1 20.0 + - + -
154C VAL* 4.0 10.9 - - + +
155C VAL 3.5 4.5 - - - +
156C LEU* 3.6 21.5 - - + -
169C THR* 1.3 74.3 - - - +
171C GLY* 1.3 88.2 + - - +
172C ILE* 4.7 1.0 - - - +
193C ASP 4.5 2.3 - - - +
194C ALA* 3.9 9.8 - - - -
195C SER 4.7 0.7 + - - -
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Residues in contact with GLY 171 (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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170B GLN* 4.7 1.8 - - - -
154C VAL* 3.4 1.6 - - - -
155C VAL* 2.9 28.3 + - - -
170C GLN* 1.3 94.0 + - - +
172C ILE* 1.3 64.9 + - - +
193C ASP* 3.3 15.5 - - - -
194C ALA* 3.8 11.9 - - - +
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Residues in contact with ILE 172 (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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47B TYR* 4.1 11.2 - - + -
156B LEU* 4.3 4.3 - - + -
168B ILE* 3.6 45.1 - - + +
169B THR 3.8 2.5 - - - -
170B GLN* 3.7 33.9 - - + +
152C GLY* 3.6 23.8 - - - +
153C ASP 3.0 9.9 - - - +
154C VAL* 4.1 7.4 - - + -
155C VAL* 3.7 7.1 - - - +
171C GLY* 1.3 79.9 - - - +
173C ILE* 1.3 70.7 + - - +
174C SER 3.0 4.9 + - - -
192C THR* 3.1 16.7 + - - -
193C ASP* 2.8 23.0 + - - +
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Residues in contact with ILE 173 (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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149C PRO* 3.8 26.9 - - + -
150C HIS 3.5 26.2 - - - +
151C ILE* 3.3 9.7 - - - +
152C GLY* 2.8 26.3 + - - -
153C ASP* 2.7 23.8 + - + +
155C VAL* 3.6 24.9 - - + -
172C ILE* 1.3 74.9 - - - +
174C SER* 1.3 58.2 + - - +
175C ALA 3.4 24.0 - - - +
176C THR* 4.2 10.8 - - + -
190C LEU* 4.5 16.6 - - + -
191C GLN 3.7 5.6 - - - +
192C THR* 4.8 0.9 - - - +
205C LEU* 5.6 2.0 - - + -
213C MET* 4.6 6.7 - - - -
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Residues in contact with SER 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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166B GLN 4.3 1.0 - - - +
167B THR* 3.9 15.8 - - - -
168B ILE* 2.8 44.9 + - - +
169B THR* 4.2 2.3 - - - +
151C ILE* 3.6 11.3 - - - +
172C ILE 3.0 2.9 + - - -
173C ILE* 1.3 73.7 - - - +
175C ALA* 1.3 60.0 + - - +
191C GLN* 2.7 28.0 + - - -
192C THR 3.6 1.2 - - - -
193C ASP* 3.5 27.2 + - - +
231C GLY 4.7 0.5 + - - -
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Residues in contact with ALA 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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166B GLN 3.9 3.8 - - - +
167B THR* 5.1 0.2 - - - -
151C ILE* 4.1 12.1 - - + -
173C ILE* 3.4 9.5 + - - +
174C SER* 1.3 81.2 - - - +
176C THR* 1.3 71.9 + - - +
178C ARG* 3.4 40.6 - - + +
189C PHE 4.8 0.2 - - - -
190C LEU* 3.7 1.6 - - - -
191C GLN* 3.1 32.5 + - + +
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Residues in contact with THR 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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149C PRO* 4.9 13.2 - - + +
151C ILE* 4.1 24.5 - - + +
173C ILE* 4.2 5.8 - - + -
175C ALA* 1.3 83.3 - - - +
177C GLY* 1.3 64.8 + - - +
178C ARG* 3.3 12.1 + - - +
189C PHE 3.6 6.7 - - - -
190C LEU* 3.7 19.3 - - + -
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Residues in contact with GLY 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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176C THR* 1.3 75.7 - - - +
178C ARG* 1.3 63.6 + - - +
179C ILE* 4.0 7.4 + - - +
188C ASN* 3.6 28.4 - - - +
189C PHE 3.1 6.5 + - - -
190C LEU* 5.6 0.2 - - - +
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Residues in contact with ARG 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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164B LEU* 3.1 29.3 + - - +
165B GLY* 3.2 27.7 + - - -
166B GLN* 2.9 27.8 + - - +
167B THR* 3.6 3.2 + - - -
175C ALA* 3.4 22.4 - - + +
176C THR 4.3 8.3 + - - +
177C GLY* 1.3 79.9 - - - +
179C ILE* 1.3 63.8 + - - +
180C GLY 4.0 8.3 - - - +
188C ASN* 3.3 7.6 - - - -
189C PHE* 2.8 38.8 + - + +
191C GLN* 2.9 36.0 + - + +
234C PHE* 4.3 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
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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