Contacts of the strand formed by residues 160 - 168 (chain C) in PDB entry 4I6N
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 PHE 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C LEU* 3.8 31.6 - - + -
53C PHE 3.4 1.3 - - - -
54C ARG* 3.7 33.9 - - + -
158C ASP 4.2 13.0 - - - -
159C VAL* 1.3 75.3 - - - +
161C HIS* 1.3 57.7 + - - +
215C ARG* 3.7 57.9 - - + -
40D GLN* 5.7 2.2 - - - -
73D LEU* 3.9 19.5 - - + -
74D ARG 3.9 18.8 + - - +
75D GLY* 3.0 3.7 - - - -
101D GVE 2.9 34.3 + - - +
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Residues in contact with HIS 161 (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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51C PHE 3.5 1.7 - - - +
52C LEU* 3.1 25.2 - - - -
53C PHE* 2.9 32.3 + + + +
55C TRP* 3.9 18.4 - + + -
79C GLN* 3.4 24.9 - - - -
85C CYS* 3.7 2.1 - - + +
160C PHE* 1.3 74.2 - - - +
162C PHE* 1.3 79.3 + - - +
163C VAL* 3.6 17.1 - - + +
176C ASP* 2.9 28.9 + - - -
177C GLY 4.5 1.3 - - - -
178C LEU* 3.9 3.4 - - + +
101D GVE 3.1 43.3 + - - +
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Residues in contact with PHE 162 (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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9C ILE 3.3 25.8 - - - -
11C SER* 3.9 14.1 - - - -
16C PHE* 3.5 27.4 - + - -
50C ILE* 3.7 18.4 - - + -
51C PHE 3.4 1.6 - - - -
52C LEU* 3.5 31.0 - - + -
79C GLN* 4.8 0.5 - - - +
85C CYS* 3.7 24.4 - - - +
86C ALA* 3.5 31.9 - - + -
89C ALA* 3.8 15.4 - - + +
161C HIS* 1.3 92.6 + - - +
163C VAL* 1.3 61.1 + - - +
177C GLY 5.2 1.7 + - - -
219C MSE 4.2 5.2 - - + -
75D GLY* 3.6 14.8 - - - -
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Residues in contact with VAL 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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50C ILE* 3.4 5.9 - - - +
51C PHE* 2.8 43.8 + - + +
53C PHE* 3.7 19.1 - - + -
89C ALA* 4.2 4.5 - - - -
161C HIS* 3.6 26.2 - - + +
162C PHE* 1.3 80.6 - - - +
164C THR* 1.3 61.7 + - - +
165C TYR* 3.8 30.3 - - + +
174C GLU* 4.6 6.3 - - + +
175C LEU 3.7 11.4 - - - +
176C ASP* 3.7 22.4 - - + +
205C LYS* 4.9 0.4 - - - -
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Residues in contact with THR 164 (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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49C PHE 3.3 4.3 - - - -
50C ILE* 3.6 14.9 - - - +
89C ALA* 2.6 30.2 + - - +
93C LEU* 3.6 33.0 - - + +
163C VAL* 1.3 74.6 - - - +
165C TYR* 1.3 71.8 + - - +
166C VAL* 4.3 1.3 - - + -
174C GLU* 3.4 5.4 - - - +
175C LEU* 2.7 59.4 + - + -
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Residues in contact with TYR 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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48C GLY* 3.1 7.3 - - - -
49C PHE* 2.9 49.7 + - + +
51C PHE* 3.7 21.7 - - + -
163C VAL* 3.8 8.8 - - + +
164C THR* 1.3 73.7 - - - +
166C VAL* 1.3 62.4 + - - +
172C VAL* 5.3 0.7 - - + -
173C TYR 3.3 4.5 - - - +
174C GLU* 2.7 46.0 + - + -
185C LEU* 3.7 26.0 - - + -
194C TRP* 3.6 6.9 - - + -
198C ALA* 3.8 24.9 - - + -
201C ALA* 4.2 7.8 - - + -
202C ILE* 3.7 31.1 + - + +
205C LYS* 3.7 16.3 - - - -
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Residues in contact with VAL 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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47C HIS 3.7 12.1 - - - +
93C LEU* 4.3 13.0 - - + +
96C ASN* 4.2 26.2 - - + +
97C CYS* 5.4 2.2 - - - +
164C THR* 4.3 5.8 - - + -
165C TYR* 1.3 77.2 - - - +
167C PRO* 1.3 83.9 - - + +
168C VAL* 4.3 7.4 - - + -
173C TYR* 2.9 32.9 + - + +
175C LEU* 3.6 34.5 - - + -
194C TRP* 4.1 4.4 - - - -
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Residues in contact with PRO 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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46C ILE 5.2 1.1 - - - +
47C HIS* 3.7 8.7 - - - +
96C ASN 4.7 4.2 - - - +
166C VAL* 1.3 95.9 - - + +
168C VAL* 1.3 65.6 + - - +
169C ASN 4.3 4.7 - - - +
171C GLY 3.2 11.2 - - - +
172C VAL* 4.3 2.2 - - + -
188C VAL* 4.9 4.5 - - + -
194C TRP* 3.5 57.9 - - + +
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Residues in contact with VAL 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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73C ASP* 3.5 38.3 - - + +
74C VAL* 4.2 4.9 - - + -
96C ASN* 3.8 37.2 - - + +
166C VAL* 3.8 7.8 + - + -
167C PRO* 1.3 80.8 - - - +
169C ASN* 1.3 77.1 + - + +
171C GLY* 2.8 21.6 + - - +
173C TYR* 3.7 23.6 + - + -
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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