Contacts of the strand formed by residues 160 - 168 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.9 32.3 - - + -
53A PHE 3.4 1.3 - - - -
54A ARG* 3.8 33.7 - - + -
152A GLN* 5.0 3.4 + - - +
158A ASP 4.0 13.9 - - - -
159A VAL* 1.3 73.2 - - - +
161A HIS* 1.3 59.1 + - - +
215A ARG* 3.7 54.1 - - + -
40B GLN* 5.3 5.8 - - - -
73B LEU* 4.1 20.2 - - + -
74B ARG 3.9 20.0 + - - +
75B GLY* 3.2 1.8 - - - -
101B GVE 2.9 31.5 + - - +
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Residues in contact with HIS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE 3.5 1.6 - - - +
52A LEU* 3.1 24.7 - - - -
53A PHE* 2.9 32.6 + + + +
55A TRP* 3.9 17.7 - + + -
79A GLN* 3.3 26.2 - - - -
85A CYS* 3.7 1.9 - - + +
159A VAL 3.8 0.2 + - - -
160A PHE* 1.3 72.2 - - - +
162A PHE* 1.3 78.8 + - - +
163A VAL* 3.6 17.7 - - + +
176A ASP* 2.8 27.5 + - - -
177A GLY 4.6 1.1 - - - -
178A LEU* 3.9 2.9 - - + +
101B GVE 3.1 43.2 + - - +
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE 3.4 26.0 - - - -
11A SER* 3.8 17.0 - - - -
16A PHE* 3.5 25.1 - + - -
50A ILE* 3.8 19.1 - - + -
51A PHE 3.4 1.3 - - - -
52A LEU* 3.5 31.4 - - + -
79A GLN* 4.9 0.5 - - - +
85A CYS* 3.7 19.9 - - - +
86A ALA* 3.5 29.6 - - + -
89A ALA* 3.8 23.5 - - + +
161A HIS* 1.3 91.4 + - - +
163A VAL* 1.3 63.2 + - - +
175A LEU 5.1 0.2 - - - +
177A GLY 5.2 2.1 + - - -
219A MSE 4.2 4.9 - - + -
75B GLY* 3.6 15.0 - - - -
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.3 6.6 - - - +
51A PHE* 2.8 42.1 + - + +
53A PHE* 3.5 26.9 - - + -
89A ALA* 4.2 3.1 - - - -
161A HIS* 3.6 19.3 - - + +
162A PHE* 1.3 79.5 - - - +
164A THR* 1.3 63.5 + - - +
165A TYR* 3.8 30.1 - - + +
174A GLU* 4.6 6.5 - - + -
175A LEU 3.7 11.0 - - - +
176A ASP* 3.7 19.5 - - + +
205A LYS* 5.1 0.7 - - - -
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Residues in contact with THR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE 3.3 6.7 + - - -
50A ILE* 4.1 3.5 - - - +
89A ALA* 2.7 32.6 + - - +
93A LEU* 3.6 41.2 - - + +
163A VAL* 1.3 74.9 + - - +
165A TYR* 1.3 71.0 + - - +
166A VAL* 4.4 1.3 - - + -
173A TYR 3.6 0.3 - - - +
174A GLU* 3.4 4.5 - - - +
175A LEU* 2.7 59.3 + - + -
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY* 3.1 7.4 - - - -
49A PHE* 2.8 44.6 + - + +
51A PHE* 3.8 11.7 - - + -
163A VAL* 3.8 19.3 - - + +
164A THR* 1.3 75.8 - - - +
166A VAL* 1.3 62.7 + - - +
172A VAL* 5.2 0.2 - - + -
173A TYR 3.3 4.0 - - - -
174A GLU* 2.6 45.6 + - + -
185A LEU* 3.7 26.5 - - + -
194A TRP* 3.7 3.6 - - + -
198A ALA* 3.8 25.8 - - + -
201A ALA* 3.9 10.2 - - + +
202A ILE* 3.6 38.2 + - + +
205A LYS* 3.9 14.0 - - - -
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A HIS 3.5 20.2 - - - +
74A VAL* 5.6 0.4 - - + -
93A LEU* 4.2 24.5 - - + +
96A ASN* 4.2 20.0 - - + +
97A CYS* 5.5 1.3 - - - -
164A THR* 4.4 7.0 - - + -
165A TYR* 1.3 74.1 - - - +
167A PRO* 1.4 70.3 - - + +
168A VAL* 4.3 9.4 - - + -
172A VAL* 4.3 0.2 - - - -
173A TYR* 2.8 39.9 + - + +
175A LEU* 3.8 28.3 - - + -
194A TRP* 4.2 4.8 - - - -
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Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE 5.1 1.3 - - - +
47A HIS* 3.7 10.5 - - - +
96A ASN 4.7 4.2 - - - +
166A VAL* 1.4 95.6 - - + +
168A VAL* 1.3 66.5 - - - +
169A ASN 5.3 3.4 - - - +
171A GLY 3.4 10.3 - - - +
172A VAL* 4.2 2.2 - - - -
188A VAL* 6.1 1.3 - - + -
194A TRP* 3.7 54.9 - - + +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASP* 3.5 37.0 - - + +
74A VAL* 4.4 8.1 - - + -
96A ASN* 3.8 37.5 - - + +
166A VAL* 4.0 10.2 + - + -
167A PRO* 1.3 80.0 - - - +
169A ASN* 1.3 76.0 + - + +
170A ASP* 4.5 0.2 - - - +
171A GLY* 3.0 22.5 + - - +
173A TYR* 3.9 15.1 + - + -
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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