Contacts of the strand formed by residues 164 - 173 (chain B) in PDB entry 4ROE
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 GLN 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A VAL 5.0 1.7 - - - +
374A PRO* 3.2 38.2 - - - +
162B VAL* 3.5 28.3 + - - +
163B PRO* 1.3 72.6 + - - +
165B LEU* 1.3 63.8 + - - +
166B GLN* 3.5 21.5 + - - +
260B GLY* 3.3 1.8 - - - -
261B SER 2.8 36.3 + - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PRO 3.9 4.2 + - - +
164B GLN* 1.3 72.7 - - - +
166B GLN* 1.3 64.1 + - - +
168B ILE* 4.2 8.7 - - + -
225B LYS* 3.3 39.1 - - - +
227B GLU* 3.8 11.7 - - - +
258B MET* 4.0 19.3 - - + -
259B VAL 3.5 12.6 - - - +
260B GLY* 4.5 2.7 - - - -
318B ARG* 3.7 46.2 - - + +
321B ILE* 4.4 26.2 - - + -
322B TYR* 5.3 2.0 - - + +
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Residues in contact with GLN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLN* 3.6 26.7 + - - +
165B LEU* 1.3 75.4 - - - +
167B ASN* 1.3 59.2 + - - +
223B GLY 4.4 0.7 - - - +
224B ALA 4.2 1.0 - - - +
225B LYS* 3.0 44.9 + - - +
259B VAL* 2.8 17.9 + - + +
260B GLY 4.5 0.7 - - - -
261B SER* 2.9 33.3 + - - +
15T T 3.2 19.1 - - + +
16T A 3.5 35.5 - - - +
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Residues in contact with ASN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU 3.8 0.4 - - - -
166B GLN* 1.3 81.1 - - - +
168B ILE* 1.3 69.6 + - - +
169B VAL* 3.9 7.0 - - - +
222B THR* 4.5 0.3 - - - -
223B GLY* 2.9 34.1 + - - -
224B ALA 3.4 7.7 + - - -
257B ASN 4.7 0.2 - - - -
258B MET* 3.6 1.0 - - - -
259B VAL* 2.9 37.6 + - + +
14T A 3.0 37.1 + - - -
15T T 3.3 36.7 + - - +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 4.2 20.4 - - + -
167B ASN* 1.3 83.0 + - - +
169B VAL* 1.3 65.0 + - - +
170B SER 4.1 0.2 - - - -
221B CYS 3.5 9.7 - - - +
222B THR* 3.5 1.4 - - - -
223B GLY 3.5 16.3 + - - -
224B ALA* 3.0 21.2 + - - +
226B SER 3.7 21.5 - - - +
227B GLU* 4.4 2.9 - - - -
230B SER* 3.8 18.9 + - - +
255B ILE* 3.7 40.6 - - + -
257B ASN 3.5 2.7 - - - +
258B MET* 3.5 33.2 - - + -
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ASN* 3.9 6.3 - - - +
168B ILE* 1.3 76.6 - - - +
170B SER* 1.3 56.2 + - - +
220B VAL* 3.9 12.3 - - + -
221B CYS 3.4 3.1 - - - +
222B THR* 4.0 7.4 - - + -
255B ILE* 3.7 2.8 - - - +
256B GLN* 2.7 41.6 + - + -
257B ASN* 2.9 23.2 + - + +
16N T 3.4 22.9 - - + +
17N A 3.6 30.7 - - + +
14T A 3.6 23.8 - - + +
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ILE 4.1 0.2 - - - -
169B VAL* 1.3 73.3 - - - +
171B THR* 1.3 63.0 + - - +
220B VAL* 3.4 6.2 - - - +
221B CYS* 2.8 46.0 + - - +
230B SER* 2.8 25.2 + - - -
234B ALA* 4.5 0.3 - - - +
253B PHE* 3.3 27.0 - - - -
254B LYS 3.2 13.9 - - - -
255B ILE* 4.0 5.8 - - - -
256B GLN* 4.1 1.6 - - - +
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Residues in contact with THR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B SER* 1.3 79.0 - - - +
172B VAL* 1.4 66.3 + - - +
219B MET 3.2 12.8 - - - +
220B VAL* 4.1 6.3 - - + -
221B CYS* 5.0 0.4 - - - +
234B ALA* 6.2 0.4 - - - -
252B ASP 4.5 1.9 + - - -
253B PHE* 3.4 5.2 - - - -
254B LYS* 2.9 36.3 + - - +
256B GLN* 2.8 37.7 + - + -
17N A 3.7 33.2 + - + +
18N A 5.2 4.7 - - - -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B THR* 1.4 76.7 - - - +
173B ASN* 1.3 58.9 + - - +
174B LEU* 4.4 7.0 - - + -
218B LYS* 3.7 4.6 - - - +
219B MET* 2.9 69.5 + - + +
221B CYS* 6.4 0.2 - - + -
234B ALA* 4.4 3.4 - - + -
250B PHE* 3.6 37.9 - - + -
251B LEU 3.3 28.5 - - - +
252B ASP 4.4 3.1 - - - -
253B PHE* 3.9 12.8 - - + +
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Residues in contact with ASN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B VAL* 1.3 72.1 - - - +
174B LEU* 1.3 64.1 + - - +
175B GLY* 2.9 24.3 + - - +
176B CYS 4.7 0.3 + - - -
216B SER 4.7 3.1 - - - +
217B GLY* 4.0 10.6 - - - +
218B LYS* 3.8 31.8 - - + +
249B LYS 3.6 0.9 - - - +
251B LEU* 2.8 56.2 + - + +
252B ASP* 4.4 13.1 + - + +
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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