Contacts of the strand formed by residues 136 - 143 (chain F) in PDB entry 1H4O
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 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F GLY* 3.5 27.8 - - - +
7F ASP 3.5 2.0 - - - +
8F ALA* 3.9 23.8 - - + +
132F VAL* 3.3 2.4 - - - -
133F GLN 2.8 38.5 + - - +
134F ASP* 3.9 6.5 - - + +
135F GLY* 1.3 81.9 - - - +
137F VAL* 1.3 70.9 + - - +
138F LYS* 3.3 25.3 + - - +
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Residues in contact with VAL 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F ILE* 4.0 22.2 - - + -
4F LYS 4.0 9.4 - - - +
5F VAL* 3.5 12.8 - - - +
6F GLY* 2.7 30.7 + - - -
7F ASP 2.9 20.6 + - - +
9F ILE* 4.6 9.0 - - - +
130F MET* 4.0 28.5 - - + -
131F VAL 3.6 5.4 - - - +
132F VAL* 4.5 4.5 - - + +
136F ILE* 1.3 71.6 - - - +
138F LYS* 1.3 61.2 + - - +
139F ALA 3.6 23.6 - - - +
140F LEU* 4.2 10.3 - - + -
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Residues in contact with LYS 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 3.9 18.4 - - + +
6F GLY* 6.0 1.2 - - - -
131F VAL* 2.8 22.1 + - + +
133F GLN* 3.6 36.8 - - + +
136F ILE* 3.7 30.8 - - + +
137F VAL* 1.3 79.3 - - - +
139F ALA* 1.3 62.4 + - + +
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Residues in contact with ALA 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 3.9 5.6 - - - -
130F MET* 3.2 10.0 - - - +
131F VAL* 3.0 39.3 + - + +
137F VAL* 3.6 3.4 - - - +
138F LYS* 1.3 80.8 - - - +
140F LEU* 1.3 61.6 + - - +
141F ASN* 4.3 0.9 - - - -
160F GLN* 3.9 33.2 - - + +
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F ILE* 3.5 34.1 - - + +
4F LYS* 4.2 10.3 - - - -
5F VAL* 3.9 16.3 - - + +
110F LEU* 5.1 2.2 - - + -
128F PHE* 4.6 4.9 - - + -
129F SER 3.6 6.5 - - - +
130F MET* 3.8 28.7 - - + -
137F VAL* 4.2 5.4 - - + -
139F ALA* 1.3 76.8 - - - +
141F ASN* 1.3 68.7 + - - +
142F VAL* 4.1 24.1 + - + -
160F GLN* 5.3 0.5 + - - +
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Residues in contact with ASN 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F PHE* 3.0 6.6 - - - +
129F SER* 2.8 58.9 + - - +
139F ALA 5.1 0.6 - - - -
140F LEU* 1.3 80.2 - - - +
142F VAL* 1.3 61.2 + - - +
151F CYS* 3.3 35.0 + - - +
152F SER* 4.2 0.9 - - - -
156F ASN* 3.4 5.9 + - - +
157F ILE* 4.1 8.5 - - - +
160F GLN* 2.8 44.9 + - - -
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Residues in contact with VAL 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 4.0 21.5 - - + -
126F LYS* 4.1 30.7 - - + +
127F ARG 3.8 8.7 - - - +
128F PHE* 4.1 4.0 - - + -
140F LEU* 4.1 25.0 + - + -
141F ASN* 1.3 76.2 - - - +
143F GLU* 1.3 78.8 + - - +
144F PRO* 3.1 5.2 - - - +
151F CYS* 3.5 10.8 - - - -
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Residues in contact with GLU 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F ARG* 3.0 28.4 + - + +
128F PHE* 4.8 0.2 - - - +
141F ASN 4.2 0.4 - - - -
142F VAL* 1.3 79.0 - - - +
144F PRO* 1.3 67.4 - - + +
145F ASP* 4.1 2.9 - - - +
146F GLY* 2.9 36.7 + - - +
147F THR 4.0 1.3 - - - +
148F GLY* 3.0 30.1 - - - +
149F LEU 3.7 0.2 + - - -
150F THR* 2.6 43.2 + - - +
151F CYS* 4.0 2.8 - - - -
152F SER* 2.7 32.2 + - - +
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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