Contacts of the strand formed by residues 157 - 163 (chain A) in PDB entry 4RUH
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 ASN 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LEU 3.4 4.5 - - - -
86A GLY* 3.1 21.3 - - - +
87A SER* 3.0 9.7 + - - +
88A ASP* 2.6 55.2 + - - +
91A LYS* 3.3 18.9 + - - +
92A LYS 2.9 9.5 + - - -
93A THR* 3.3 29.3 + - + +
94A VAL 2.8 26.7 + - - -
156A VAL* 1.3 77.4 - - - +
158A VAL* 1.3 58.9 + - - +
159A ARG* 4.8 0.2 - - - +
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Residues in contact with VAL 158 (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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83A GLY 3.6 1.0 - - - +
85A LEU* 2.6 53.8 + - + +
94A VAL* 3.5 5.4 - - + +
96A ILE* 3.7 28.5 - - + -
144A LEU* 3.7 26.7 - - + -
154A ILE* 4.6 0.9 - - + -
156A VAL* 3.9 18.8 - - + +
157A ASN* 1.3 79.8 - - - +
159A ARG* 1.3 70.8 + - - +
160A PHE* 3.8 28.9 - - + +
467A LEU* 5.0 2.0 - - + -
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Residues in contact with ARG 159 (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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83A GLY 3.4 2.9 - - - -
84A ARG* 4.0 17.8 - - - +
85A LEU 3.6 7.3 - - - +
86A GLY 2.8 28.5 + - - -
87A SER* 4.1 15.4 - - - +
93A THR* 3.6 26.9 + - + +
94A VAL 2.8 13.1 + - - +
95A CYS* 3.4 9.7 - - + -
96A ILE 3.1 22.6 + - - +
157A ASN* 4.3 1.4 - - - +
158A VAL* 1.3 91.5 + - - +
160A PHE* 1.3 64.4 + - - +
161A CYS 3.6 0.7 + - - -
184A PHE* 3.6 50.5 + - + +
187A ASP* 5.4 9.7 + - - +
188A VAL* 4.2 15.0 - - + -
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Residues in contact with PHE 160 (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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52A VAL* 3.6 28.0 - - + -
55A LEU* 4.9 0.4 - - + -
81A LEU* 3.4 13.2 - - + +
82A LEU* 3.4 4.0 - - - -
83A GLY* 2.9 39.8 + - - +
85A LEU* 4.0 10.1 - - + -
96A ILE* 3.6 25.8 - - + +
137A VAL* 5.8 1.8 - - + -
140A TRP* 4.6 6.1 - - + -
141A ILE* 3.7 24.9 - - + -
144A LEU* 3.3 34.5 - - + -
158A VAL* 3.8 13.9 - - + -
159A ARG* 1.3 72.7 - - - +
161A CYS* 1.3 57.9 + - - +
162A LEU* 4.0 26.9 - - + -
184A PHE* 3.6 6.8 - - - -
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Residues in contact with CYS 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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80A ILE* 4.4 2.9 - - - -
81A LEU 3.4 3.6 - - - -
82A LEU* 4.1 16.4 - - + -
95A CYS* 4.6 1.8 - - - -
96A ILE 2.9 11.6 + - - +
97A TYR* 3.1 33.5 - - - -
98A GLY 3.4 0.5 + - - -
159A ARG 3.6 0.4 + - - -
160A PHE* 1.3 73.5 - - - +
162A LEU* 1.3 60.9 + - - +
173A LEU* 3.7 30.1 - - - -
176A LEU* 4.9 0.2 - - - -
185A PHE* 4.1 28.7 - - + -
424A PHE* 4.2 18.2 - - + -
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Residues in contact with LEU 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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45A MET* 3.3 11.2 - - + +
48A ALA* 4.4 13.0 - - + -
52A VAL* 5.4 2.9 - - + -
80A ILE* 3.8 5.6 - - - +
81A LEU* 2.9 61.6 + - + -
96A ILE* 4.4 4.7 - - + +
97A TYR 4.4 1.8 - - - -
98A GLY* 3.2 34.1 - - - +
100A LEU* 4.9 7.2 - - + -
137A VAL* 4.3 24.7 - - + -
141A ILE* 5.7 2.0 - - + -
160A PHE* 4.0 33.4 - - + -
161A CYS* 1.3 77.4 - - - +
163A GLU* 1.3 61.6 + - - +
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Residues in contact with GLU 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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45A MET* 3.9 7.6 - - - -
79A PRO 4.9 0.7 - - - -
80A ILE* 4.5 16.1 - - + +
97A TYR* 2.6 25.6 + - + +
98A GLY 3.2 3.4 + - - -
99A HIS* 3.4 10.9 - - + -
100A LEU* 2.8 35.3 + - - +
161A CYS 4.4 0.4 + - - -
162A LEU* 1.3 74.8 - - - +
164A GLY* 1.3 53.5 + - - +
165A MET* 3.2 19.9 + - - +
166A GLU* 3.3 14.3 + - - +
170A SER* 2.4 34.5 + - - -
171A GLU 5.2 0.9 - - - +
173A LEU* 3.3 23.9 - - + +
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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