Contacts of the strand formed by residues 171 - 179 (chain K) in PDB entry 6CXI
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 SER 171 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166K VAL* 4.3 3.4 - - - +
169K GLY 5.0 1.0 + - - -
170K GLY* 1.3 74.4 + - - -
172K ILE* 1.3 61.7 + - - +
173K THR* 4.4 2.7 - - - -
226K ILE 3.6 3.6 - - - -
227K THR* 3.6 22.2 - - - +
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Residues in contact with ILE 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K GLY* 3.7 15.3 - - - -
165K GLU 3.7 25.6 - - - +
166K VAL* 3.9 20.2 - - + -
171K SER* 1.3 75.6 - - - +
173K THR* 1.3 67.0 + - - +
174K PHE* 3.5 35.6 - - + -
224K LEU 3.8 1.2 - - - +
225K HIS* 3.9 0.5 - - - -
226K ILE* 2.9 65.3 + - + +
227K THR* 5.2 0.2 - - - +
254K LEU* 4.0 11.2 - - + -
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Residues in contact with THR 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K SER* 5.4 2.1 - - - -
172K ILE* 1.3 77.9 + - - +
174K PHE* 1.3 79.9 + - - +
175K SER* 5.2 2.2 - - - -
223K GLU* 4.4 14.1 - - + +
224K LEU 3.6 4.5 - - - +
225K HIS* 3.4 35.3 + - + +
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Residues in contact with PHE 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K PRO* 5.0 4.7 - - + -
162K GLN* 3.2 27.6 - - + +
163K ASP 4.2 0.2 - - - -
164K GLY* 3.6 26.0 - - - -
172K ILE* 3.5 28.5 - - + -
173K THR* 1.3 84.6 - - - +
175K SER* 1.3 61.8 + - - +
191K TRP* 4.4 7.0 - - + -
223K GLU* 3.3 4.3 - - - +
224K LEU* 2.7 56.4 + - + -
226K ILE* 4.5 7.6 - - + -
252K PHE* 3.5 32.1 - + + -
253K ASN 4.5 3.1 - - - -
254K LEU* 3.8 26.0 - - + -
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Residues in contact with SER 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159K MET* 4.6 8.8 - - - +
160K ARG 4.5 2.1 - - - +
161K PRO* 3.7 20.1 - - - +
162K GLN 5.0 0.9 + - - +
173K THR* 4.4 3.5 + - - -
174K PHE* 1.3 77.5 - - - +
176K ALA* 1.3 62.6 + - - +
177K ARG* 5.7 2.0 - - - +
191K TRP* 4.8 2.9 - - - -
221K LEU* 4.0 12.9 - - - +
222K PHE 3.3 10.1 - - - -
223K GLU* 3.8 17.5 - - - -
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Residues in contact with ALA 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K PHE* 3.2 35.9 - - + -
159K MET 3.8 5.6 - - - +
161K PRO* 4.2 11.4 - - + -
175K SER* 1.3 75.3 - - - +
177K ARG* 1.3 63.2 + - - +
178K VAL* 5.1 0.7 - - - -
191K TRP* 4.6 2.2 - - + -
220K TYR 3.8 2.3 - - - +
221K LEU* 3.6 4.3 - - - +
222K PHE* 2.9 42.2 + - + +
239K CYS* 4.3 7.0 - - - -
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Residues in contact with ARG 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K PHE* 3.5 5.5 - - - -
158K VAL* 2.9 38.2 + - + +
159K MET* 3.5 43.4 + - + +
175K SER* 5.7 2.0 - - - +
176K ALA* 1.3 77.4 - - - +
178K VAL* 1.3 62.9 + - - +
217K SER* 4.9 9.1 + - - -
219K VAL* 4.4 21.9 - - + +
220K TYR 4.0 3.1 - - - -
221K LEU* 4.0 17.2 - - + +
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Residues in contact with VAL 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K LEU* 3.4 44.4 - - + +
157K PHE* 4.3 4.7 - - + +
158K VAL* 4.7 2.0 - - - +
177K ARG* 1.3 79.0 - - - +
179K ALA* 1.3 64.4 + - - +
180K GLY* 3.8 0.7 + - - -
187K PRO* 3.6 23.7 - - + +
219K VAL* 2.9 20.7 - - - +
220K TYR 3.1 22.2 + - - +
222K PHE* 4.0 15.9 - - + -
241K VAL* 3.8 27.8 - - + -
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Residues in contact with ALA 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K LEU* 3.4 27.3 - - + +
158K VAL* 3.8 25.0 - - + +
178K VAL* 1.3 75.0 - - - +
180K GLY* 1.3 65.0 + - - +
217K SER 5.5 1.6 - - - +
219K VAL* 4.1 17.5 - - + -
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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