Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 4OHN
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 GLN 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASN* 3.6 2.6 - - - +
126A GLU* 1.3 71.8 - - - +
128A VAL* 1.3 63.3 + - - +
154A SER* 5.8 0.2 - - - -
155A SER* 3.8 11.5 + - - -
156A GLY* 3.4 22.7 - - - +
159A ASP* 3.8 19.3 - - - +
182A PHE* 5.5 1.2 - - - -
198A LEU* 4.2 8.0 - - + +
199A ILE* 3.6 21.7 + - - -
200A ASP* 3.2 26.2 + - - +
221A THR* 3.8 15.8 - - - +
222A VAL* 4.5 6.1 + - - +
224A LEU* 3.8 28.8 + - + +
225A GLU 5.5 5.2 + - - +
227A GLU* 3.2 29.0 + - - +
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Residues in contact with VAL 128 (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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127A GLN* 1.3 73.8 - - - +
129A LEU* 1.3 59.4 + - - +
130A VAL* 4.4 1.8 - - + -
197A LEU 3.4 1.0 - - - +
198A LEU* 3.4 10.0 - - - +
199A ILE* 2.9 55.6 + - + +
200A ASP 4.2 0.2 - - - -
201A ARG* 3.8 40.2 - - + +
204A ALA* 4.4 0.7 - - + -
219A VAL* 3.7 24.7 - - + -
220A PHE 3.3 15.5 - - - +
221A THR* 3.6 27.8 - - + +
222A VAL* 5.3 1.1 - - - +
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Residues in contact with LEU 129 (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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128A VAL* 1.3 74.0 - - - +
130A VAL* 1.3 60.7 + - - +
131A THR* 4.2 6.5 - - + -
140A ALA* 4.6 4.5 - - - -
143A MET* 3.5 30.7 - - + -
148A LEU* 3.6 31.0 - - + -
167A LEU* 4.6 9.9 - - + -
196A GLY* 3.9 3.8 - - - -
197A LEU 3.4 19.7 - - - +
198A LEU* 4.1 2.9 - - + +
219A VAL* 3.5 2.8 - - - -
220A PHE* 2.8 68.8 + - + -
222A VAL* 3.9 17.2 - - + +
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Residues in contact with VAL 130 (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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128A VAL* 4.4 0.4 - - + -
129A LEU* 1.3 75.7 - - - +
131A THR* 1.3 63.6 + - - +
186A LEU* 4.8 10.1 - - + -
189A LEU* 3.7 23.9 - - + +
196A GLY* 3.3 4.9 - - - -
197A LEU* 2.9 34.9 + - + +
199A ILE* 3.5 27.1 - - + -
204A ALA* 3.9 18.6 - - + -
208A LEU* 4.5 5.4 - - + -
217A TYR* 3.9 20.9 - - + -
218A ASN 3.2 8.3 - - - +
219A VAL* 4.1 14.4 - - + -
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Residues in contact with THR 131 (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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129A LEU* 4.2 13.0 - - + -
130A VAL* 1.3 78.8 - - - +
132A LYS* 1.3 59.2 + - - +
135A SER* 3.6 12.8 + - - -
137A ILE* 2.8 43.5 + - + +
143A MET* 4.5 1.8 - - - -
189A LEU* 4.4 1.8 - - - -
195A ASP 3.5 19.5 - - - +
196A GLY* 4.0 7.0 - - - -
217A TYR* 3.3 11.7 - - - -
218A ASN* 2.8 40.1 + - - +
220A PHE* 3.9 3.3 - - + -
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Residues in contact with LYS 132 (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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131A THR* 1.3 76.4 + - - +
133A LYS* 1.3 62.1 + - - +
134A SER* 3.6 23.3 + - - +
135A SER* 2.7 34.3 + - - +
189A LEU* 3.5 17.1 - - + +
190A LYS* 2.8 33.1 + - - +
192A ASP* 2.8 33.1 + - - +
195A ASP 4.5 3.6 + - - -
216A ASP 3.7 7.9 - - - +
217A TYR* 3.8 20.6 - - + -
218A ASN* 3.9 0.7 + - - -
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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