Contacts of the strand formed by residues 148 - 153 (chain C) in PDB entry 1HNW
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 GLY 148 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C MET* 3.6 6.5 - - - +
146C ALA* 3.4 2.5 - - - +
147C LYS* 1.3 82.2 - - - +
149C ALA* 1.3 63.0 + - - +
170C GLN 3.2 12.3 - - - -
172C ARG 3.0 15.9 - - - -
173C VAL* 3.7 4.3 - - - -
202C ILE* 3.5 3.8 - - - +
203C PHE 2.6 31.8 + - - +
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Residues in contact with ALA 149 (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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138C VAL* 4.1 14.2 - - + +
141C VAL* 3.5 33.7 - - + -
142C MET* 4.1 9.3 - - - -
148C GLY* 1.3 76.5 - - - +
150C LYS* 1.3 65.5 + - - +
151C VAL* 6.2 1.1 - - + -
169C ALA* 3.3 2.9 - - - +
170C GLN 3.0 31.7 + - - +
173C VAL* 3.4 4.6 - - - +
201C TYR 2.8 12.3 - - - +
202C ILE* 4.8 0.4 - - + -
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Residues in contact with LYS 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192A C 4.1 11.7 + - - -
4C LYS* 5.7 1.4 - - - +
138C VAL* 4.6 0.9 - - - -
149C ALA* 1.3 78.1 - - - +
151C VAL* 1.3 68.1 + - - +
152C ILE* 3.4 33.9 - - + +
167C TRP* 3.6 36.2 - - + +
168C ALA 3.4 15.0 - - - +
169C ALA* 3.7 12.6 - - + -
173C VAL* 4.5 12.1 - - + -
175C LEU* 6.2 2.2 - - - +
199C LYS 3.5 0.7 - - - +
200C ALA* 3.3 2.9 - - - -
201C TYR* 2.7 56.7 + - + +
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C VAL* 4.8 10.3 - - + -
117C ALA* 6.1 0.2 - - - -
120C VAL* 4.2 14.1 - - + -
134C ILE* 3.4 25.1 - - + -
137C ALA* 4.2 17.5 - - + -
138C VAL* 3.6 21.1 - - + +
141C VAL* 6.0 0.7 - - + -
149C ALA* 6.2 0.4 - - + -
150C LYS* 1.3 79.2 - - - +
152C ILE* 1.3 70.3 + - - +
167C TRP 2.6 31.1 - - - +
168C ALA 3.2 6.3 + - - +
198C VAL* 4.1 18.8 - - + -
199C LYS 3.0 9.9 - - - +
200C ALA* 4.8 6.1 - - + -
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Residues in contact with ILE 152 (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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1058A G 5.7 1.7 + - - +
150C LYS* 3.4 36.1 - - + +
151C VAL* 1.3 81.5 - - - +
153C VAL* 1.3 74.2 + - - +
165C THR* 4.6 10.1 - - + -
166C GLU 3.3 11.0 - - - +
167C TRP* 5.3 6.7 - - + +
197C GLY 3.7 1.0 - - - +
198C VAL* 3.2 6.8 - - - -
199C LYS* 2.7 58.7 + - + +
201C TYR* 4.2 20.4 - - + -
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Residues in contact with VAL 153 (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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120C VAL* 4.5 6.1 - - + -
124C ILE* 3.9 22.4 - - + -
130C VAL* 3.7 16.8 - - + -
134C ILE* 3.3 30.7 - - + +
151C VAL* 5.1 0.4 - - + -
152C ILE* 1.3 80.9 - - - +
154C SER* 1.3 74.7 + - - +
157C ILE* 3.9 21.8 - - + -
165C THR* 3.4 8.8 + - - +
166C GLU* 3.0 25.7 + - + -
196C LEU* 4.4 8.3 - - + -
197C GLY 3.5 7.2 - - - +
198C VAL* 4.5 4.3 - - + -
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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