Contacts of the strand formed by residues 162 - 171 (chain C) in PDB entry 6I53
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 GLU 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C MET 4.1 3.8 + - - +
161C ASP* 1.3 77.4 - - - +
163C HIS* 1.3 70.9 + - - +
204C VAL* 6.2 2.7 - - + -
229C LEU 3.4 6.3 - - - +
230C SER* 3.8 21.6 - - - -
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Residues in contact with HIS 163 (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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151C CYS* 4.9 1.3 - - - -
152C GLN 5.0 1.0 + - - -
153C LEU* 3.5 34.8 - - + +
154C GLN* 3.3 45.6 + - + +
155C LEU* 4.0 3.6 - - + +
161C ASP* 2.6 35.6 + - + -
162C GLU* 1.3 78.6 + - - +
164C SER* 1.3 58.5 + - - +
165C CYS* 3.8 9.9 - - - -
201C PHE* 3.9 19.7 - + + -
227C PHE 3.5 0.4 - - - +
228C ASP* 3.4 2.8 - - - +
229C LEU* 2.5 50.6 + - + +
231C ARG* 4.8 0.6 + - - -
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Residues in contact with SER 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C CYS* 4.6 2.0 - - - -
163C HIS* 1.3 72.6 - - - +
165C CYS* 1.3 63.6 + - - +
166C PRO* 3.4 8.8 - - - +
207C ARG* 3.4 19.5 + - - -
226C TYR* 4.1 12.6 - - - -
227C PHE 3.4 7.2 - - - -
228C ASP* 3.4 20.4 - - - -
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Residues in contact with CYS 165 (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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65C VAL* 4.9 4.0 - - - -
72C TYR* 3.6 25.1 + - + -
151C CYS* 2.0 43.3 - - - -
153C LEU* 4.2 9.9 - - - -
163C HIS* 4.4 4.9 - - - -
164C SER* 1.3 72.8 - - - +
166C PRO* 1.3 67.4 - - - +
225C VAL 3.7 1.2 - - - +
226C TYR* 4.5 0.2 - - - -
227C PHE* 3.0 37.7 + - + +
229C LEU* 4.1 22.4 - - + -
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Residues in contact with PRO 166 (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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72C TYR* 2.4 27.5 + - - -
115C ASN* 3.0 26.7 + - - +
150C GLU 4.1 10.3 - - - +
151C CYS* 4.4 7.2 - - - -
152C GLN 5.5 1.1 - - - +
164C SER 3.4 8.0 - - - +
165C CYS* 1.3 83.7 - - + +
167C LEU* 1.3 56.5 + - - +
168C GLU* 4.5 11.2 - - + +
224C SER* 4.4 5.6 - - - +
225C VAL 3.4 5.8 - - - +
226C TYR* 3.6 26.0 - - + -
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Residues in contact with LEU 167 (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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57C MET* 4.0 29.2 - - + -
72C TYR* 3.4 7.0 - - - +
74C ILE* 3.9 30.3 - - + -
76C ILE* 4.7 4.7 - - + -
113C PHE* 3.9 27.4 - - + -
115C ASN* 3.9 12.1 - - - +
147C ILE* 4.1 11.9 - - + -
149C ALA* 4.0 17.5 - - + -
166C PRO* 1.3 73.7 - - - +
168C GLU* 1.3 59.7 + - - +
169C PHE* 4.2 4.3 + - - -
224C SER* 3.5 1.6 - - - -
225C VAL* 2.7 39.2 + - + +
227C PHE* 4.2 7.2 - - + -
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Residues in contact with GLU 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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113C PHE* 3.3 9.7 - - - +
114C ARG* 2.8 49.2 + - + +
115C ASN* 3.5 16.8 + - - +
166C PRO* 4.5 15.0 - - + +
167C LEU* 1.3 73.9 - - - +
169C PHE* 1.3 61.4 + - - +
211C GLU* 4.0 13.9 - - - +
222C VAL* 4.1 12.9 - - + +
223C MET 3.3 7.2 - - - +
224C SER* 3.4 25.4 + - - +
226C TYR* 4.1 8.7 + - - -
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Residues in contact with PHE 169 (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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55C THR* 3.7 19.7 - - + -
57C MET* 3.9 13.7 - - + -
78C PHE* 3.5 22.2 - + - -
111C THR* 3.6 21.1 - - + -
112C PHE 3.3 14.4 - - - +
113C PHE* 3.6 28.0 - + + -
114C ARG* 4.2 2.2 - - - +
167C LEU 4.4 8.3 - - - -
168C GLU* 1.3 77.1 - - - +
170C SER* 1.3 63.5 + - - +
181C TYR* 4.7 4.4 - + - -
183C TRP* 3.5 34.1 - + - -
222C VAL* 3.7 2.8 - - - -
223C MET* 3.0 54.7 + - + +
225C VAL* 4.9 0.4 - - + -
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Residues in contact with SER 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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111C THR* 3.4 1.2 - - - -
112C PHE* 2.9 34.7 + - - +
114C ARG* 2.5 35.0 + - - +
169C PHE* 1.3 75.4 - - - +
171C SER* 1.3 68.3 + - - +
181C TYR* 3.8 16.2 - - - -
220C TYR* 4.7 3.6 - - - -
221C VAL 3.3 20.6 - - - -
222C VAL* 3.7 8.1 - - - -
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Residues in contact with SER 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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110C ASP* 3.5 20.6 - - - -
112C PHE* 3.3 3.0 - - - -
170C SER* 1.3 88.1 + - - +
172C TYR* 1.3 62.9 + - - +
174C TYR* 2.6 31.4 + - - +
179C ILE* 4.2 18.0 + - - +
181C TYR* 3.3 25.8 - - - -
220C TYR* 3.7 13.2 - - - +
221C VAL 4.7 1.4 + - - -
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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