Contacts of the strand formed by residues 166 - 174 (chain A) in PDB entry 1L0V
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 HIS 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A VAL* 3.7 5.4 - - - +
163A ASP 3.1 29.0 + - - +
164A ASP 3.2 7.0 + - - +
165A GLY* 1.3 78.3 - - - +
167A VAL* 1.3 91.7 + - - +
168A ARG* 3.6 37.3 - - - +
186A ASN 3.2 23.7 + - - -
371A ILE* 4.2 0.2 - - - -
372A LYS* 3.5 40.2 + - + +
373A GLY* 4.2 3.2 + - - -
413A ARG* 4.6 4.0 + - - +
417A ALA* 3.9 21.0 - - + +
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Residues in contact with VAL 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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160A ILE* 4.7 5.4 - - + -
161A LEU 3.6 12.1 - - - +
162A VAL* 4.5 6.7 - - + +
166A HIS* 1.3 100.3 + - - +
168A ARG* 1.3 65.2 + - - +
169A GLY 3.9 13.9 - - - +
185A ALA 3.8 4.7 - - - +
186A ASN* 4.0 0.5 - - - -
187A ALA* 4.1 7.4 - - - +
188A VAL* 3.9 25.6 - - + +
371A ILE* 3.9 10.4 - - + +
372A LYS 3.0 8.1 + - - +
373A GLY* 3.1 38.8 - - - +
374A LEU* 4.2 11.2 - - + +
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Residues in contact with ARG 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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161A LEU* 2.8 15.9 + - + +
163A ASP* 4.7 11.6 + - + +
166A HIS* 3.6 46.5 + - - +
167A VAL* 1.3 77.6 - - - +
169A GLY* 1.3 58.5 + - - +
184A ARG* 3.6 18.3 - - - -
185A ALA 3.2 21.5 + - - +
186A ASN* 2.9 26.8 + - - +
417A ALA* 4.4 6.3 + - - +
418A GLY 3.3 19.0 + - - -
419A ASN* 3.9 13.9 + - - +
420A GLY* 4.0 19.1 - - - +
425A ILE* 3.6 44.0 - - + -
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Residues in contact with GLY 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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8A ALA* 6.1 0.2 - - - -
160A ILE* 3.6 4.3 - - - +
161A LEU* 2.7 34.4 + - - +
167A VAL* 3.8 6.7 - - - +
168A ARG* 1.3 79.8 - - - +
170A LEU* 1.3 62.2 + - - +
183A ILE 3.1 12.1 - - - -
184A ARG* 4.2 0.2 - - - -
185A ALA* 3.4 12.7 + - - -
188A VAL* 4.4 8.2 - - - +
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Residues in contact with LEU 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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8A ALA* 4.0 17.3 - - + -
10A VAL* 3.7 29.2 - - + -
35A ILE* 3.8 21.3 - - + -
157A VAL* 4.0 17.0 - - + -
159A ASP 3.6 13.9 - - - +
160A ILE* 4.2 7.4 - - + -
161A LEU* 3.8 8.6 - - - +
169A GLY* 1.3 73.9 - - - +
171A VAL* 1.3 70.1 + - - +
172A ALA* 4.3 3.1 - - + -
182A GLN* 3.7 2.4 - - - -
183A ILE* 2.8 49.1 + - + +
188A VAL* 4.0 18.6 - - + -
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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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0A MET* 4.0 22.7 - - + -
157A VAL* 3.8 1.4 - - - +
158A LEU* 2.8 25.9 + - + +
159A ASP 3.2 9.0 + - - +
161A LEU* 3.8 21.3 - - + -
170A LEU* 1.3 78.6 - - - +
172A ALA* 1.3 69.0 + - - +
180A LEU* 4.4 13.9 - - + -
181A VAL 3.2 11.9 - - - +
182A GLN* 4.5 2.9 - - + -
429A ALA* 4.1 12.6 - - + -
432A VAL* 3.8 33.9 - - + -
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Residues in contact with ALA 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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35A ILE* 4.9 2.0 - - + -
155A HIS* 4.5 18.8 - - + -
156A PHE 3.3 15.3 - - - +
157A VAL* 3.7 20.2 - - + +
158A LEU* 3.9 1.3 - - - +
170A LEU* 4.2 7.1 - - + +
171A VAL* 1.3 75.1 - - - +
173A MET* 1.3 61.4 + - - +
174A ASN 4.2 0.2 - - - -
180A LEU* 3.4 9.3 - - - +
181A VAL* 2.9 33.6 + - + +
183A ILE* 5.4 4.7 - - + -
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Residues in contact with MET 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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155A HIS* 3.4 4.4 - - - -
156A PHE* 2.9 35.4 + - + +
158A LEU* 4.5 7.0 - - + -
172A ALA* 1.3 77.1 - - - +
174A ASN* 1.3 72.0 + - - +
175A MET* 2.9 16.5 + - - +
178A GLY* 4.0 18.8 - - - +
179A THR 3.5 14.1 - - - +
180A LEU* 3.7 13.2 - - + -
436A LEU* 4.2 21.8 - - + -
499A ASN* 6.6 0.2 - - - -
502A LEU* 3.9 28.3 - - + -
503A LEU* 4.7 15.9 - - + -
506A ILE* 5.9 0.2 - - + -
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Residues in contact with ASN 174 (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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154A GLU 4.6 1.0 - - - +
155A HIS* 3.4 38.4 + - - +
172A ALA 4.2 0.4 - - - -
173A MET* 1.3 69.3 - - - +
175A MET* 1.3 55.6 + - - +
176A MET* 3.5 7.6 + - - +
177A GLU* 3.3 32.9 + - + +
178A GLY* 2.5 37.1 + - - -
179A THR* 2.8 29.4 + - - +
181A VAL* 4.8 6.8 - - + +
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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