Contacts of the strand formed by residues 166 - 173 (chain A) in PDB entry 5NVL
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 ILE 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A TYR* 5.5 0.9 - - + +
117A LYS* 2.7 40.1 + - - +
155A MET* 3.8 36.8 - - + -
158A GLU* 6.1 0.4 - - - +
160A PHE* 4.5 13.5 - - + -
162A VAL* 3.5 29.6 - - + -
163A GLY 5.5 2.7 - - - +
164A GLU 3.1 3.7 + - - +
165A GLU* 1.3 76.3 - - - +
167A CYS* 1.3 62.2 + - - +
168A GLY 4.0 4.3 - - - +
182A ILE* 4.0 20.2 - - + -
183A TRP 3.7 6.7 - - - +
185A LYS* 4.4 1.6 + - - -
196A ILE* 3.6 26.2 - - + -
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Residues in contact with CYS 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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116A PHE* 3.4 11.3 - - + -
117A LYS* 3.0 31.8 + - - +
120A ILE* 4.0 16.5 - - + +
128A ALA* 4.2 4.3 - - - -
129A ASN* 3.8 23.3 - - - +
155A MET* 5.2 0.2 - - - -
166A ILE* 1.3 74.5 - - - +
168A GLY* 1.3 57.4 + - - +
183A TRP* 2.8 23.9 + - + +
184A ASN 3.7 26.5 - - - -
185A LYS* 3.7 24.5 - - - -
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Residues in contact with GLY 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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115A LEU 3.0 14.1 - - - -
116A PHE* 3.8 14.0 - - - -
155A MET* 3.7 14.6 - - - -
166A ILE* 3.9 2.2 - - - +
167A CYS* 1.3 82.1 - - - +
169A ALA* 1.3 61.4 + - - -
182A ILE* 3.4 6.8 - - - +
183A TRP* 2.9 25.6 + - - +
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Residues in contact with ALA 169 (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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115A LEU 2.8 32.3 + - - -
116A PHE* 3.6 1.1 - - - -
148A TRP* 3.4 20.1 - - + -
151A LEU* 3.7 26.0 - - + -
152A ILE* 4.4 1.8 - - + -
155A MET* 3.9 18.6 - - + -
168A GLY* 1.3 73.7 - - - +
170A VAL* 1.3 67.8 + - - +
181A SER 3.4 5.8 - - - +
182A ILE* 4.3 2.2 - - + +
183A TRP* 5.3 0.4 - - - -
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Residues in contact with VAL 170 (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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112A ASP* 4.5 0.9 - - + -
113A PHE 3.3 12.3 - - - +
114A HIS* 3.5 24.7 - - + +
116A PHE* 3.4 25.8 - - + -
148A TRP* 3.5 7.3 - - - -
169A ALA* 1.3 81.2 - - - +
171A VAL* 1.3 61.4 + - - +
172A SER* 3.7 22.2 - - - +
179A ILE 3.6 1.4 - - - +
180A ILE* 3.5 2.6 - - - +
181A SER* 2.9 46.4 + - - +
183A TRP* 4.0 14.6 - - + +
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Residues in contact with VAL 171 (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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104A PRO* 3.8 30.5 - - + -
107A LEU* 5.8 0.4 - - + +
112A ASP* 3.3 3.1 - - - +
113A PHE* 2.9 44.0 + - + +
144A ALA* 4.0 13.2 - - + -
148A TRP* 3.4 41.3 - - + -
170A VAL* 1.3 72.3 - - - +
172A SER* 1.3 68.2 + - - +
173A VAL* 4.2 2.8 + - + +
179A ILE 3.5 3.8 - - - +
180A ILE* 3.4 20.6 - - + -
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Residues in contact with SER 172 (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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112A ASP* 2.7 28.3 + - - -
170A VAL* 3.7 13.9 - - - +
171A VAL* 1.3 70.7 - - - +
173A VAL* 1.3 61.2 + - - +
174A ARG* 3.4 21.3 + - - +
178A ASP* 3.4 6.8 - - - +
179A ILE* 2.8 54.0 + - - +
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Residues in contact with VAL 173 (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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104A PRO* 3.1 38.4 - - + +
105A GLY* 5.4 3.1 - - - +
107A LEU* 3.9 36.6 - - + +
109A GLY 3.3 21.2 - - - +
110A HIS* 3.7 0.7 - - - -
111A SER 2.8 23.0 + - - +
141A LYS* 3.3 24.2 - - - +
144A ALA* 5.7 0.7 - - + -
171A VAL* 4.8 3.8 - - + +
172A SER* 1.3 73.3 - - - +
174A ARG* 1.3 67.1 + - - +
178A ASP* 3.5 10.8 - - - +
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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