Contacts of the strand formed by residues 141 - 148 (chain A) in PDB entry 1OKM
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 LEU 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.7 5.7 - - - -
121A VAL* 4.7 7.6 - - + -
122A HIS 3.2 12.6 - - - +
123A TRP* 3.6 8.5 - - + -
131A PHE* 3.5 33.7 - - + -
134A ALA* 4.1 6.3 - - + +
135A VAL* 4.1 19.3 - - + -
139A ASP 4.6 1.2 - - - -
140A GLY* 1.3 84.2 - - - +
142A ALA* 1.3 62.2 + - - +
143A VAL* 5.0 2.9 - - + -
198A LEU* 3.6 31.2 - - + -
206A CYS* 2.8 22.1 + - + +
207A VAL* 4.0 13.0 - - + -
208A THR* 2.9 27.8 + - - -
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Residues in contact with ALA 142 (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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79A LEU* 4.4 8.5 - - + -
84A LEU* 3.8 26.5 - - + -
88A TYR* 3.4 26.9 - - + -
122A HIS* 2.9 36.8 + - - -
141A LEU* 1.3 75.1 - - - +
143A VAL* 1.3 61.9 + - - +
208A THR 3.4 8.5 - - - +
210A ILE* 4.9 2.0 - - + -
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Residues in contact with VAL 143 (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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79A LEU* 5.6 0.9 - - - -
119A HIS* 3.7 16.2 - - + -
120A LEU 3.3 11.2 - - - +
121A VAL* 4.3 17.0 - - + -
141A LEU* 5.0 1.3 - - + -
142A ALA* 1.3 78.2 - - - +
144A LEU* 1.3 61.6 + - - +
145A GLY 3.7 1.0 + - - -
207A VAL* 3.6 24.4 - - + +
208A THR 3.4 6.1 + - - +
209A TRP* 3.5 38.0 - - + -
210A ILE* 3.1 27.7 + - - +
555A SAB 3.7 22.7 - - + +
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Residues in contact with LEU 144 (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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47A LEU* 4.0 7.2 - - + -
49A VAL* 4.6 17.3 - - + -
51A TYR* 4.3 10.1 - - - +
79A LEU* 4.7 10.3 - - + -
118A LEU 3.3 4.9 - - - +
119A HIS* 3.6 0.2 - - - -
120A LEU* 3.0 60.6 + - + +
122A HIS* 4.2 5.1 + - + -
142A ALA 4.1 0.6 + - - -
143A VAL* 1.3 72.4 - - - +
145A GLY* 1.3 59.1 + - - +
146A ILE* 3.9 1.1 + - + -
185A LEU* 4.4 14.6 - - + -
189A LEU* 6.1 0.7 - - + -
210A ILE* 3.4 35.0 - - + +
212A LEU* 3.9 28.9 - - + -
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Residues in contact with GLY 145 (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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117A GLU* 4.4 7.2 - - - -
118A LEU 3.3 6.3 - - - -
119A HIS* 4.2 12.3 - - - -
143A VAL 3.7 2.8 + - - -
144A LEU* 1.3 72.5 - - - +
146A ILE* 1.3 63.7 + - - +
147A PHE 4.3 0.2 - - - -
209A TRP* 4.5 4.4 - - - -
210A ILE 2.8 14.4 + - - -
211A VAL* 3.6 11.0 - - - +
212A LEU* 3.0 28.1 + - - +
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Residues in contact with ILE 146 (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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117A GLU* 3.3 5.0 - - - +
118A LEU* 2.8 54.3 + - + -
120A LEU* 3.8 17.7 - - + -
144A LEU* 4.5 5.6 - - + +
145A GLY* 1.3 80.7 - - - +
147A PHE* 1.3 74.4 + - - +
148A LEU* 3.5 1.6 - - - +
184A LEU 3.8 6.5 - - - +
185A LEU* 3.7 30.7 - - + -
186A PRO* 4.2 6.1 - - + -
212A LEU* 3.7 19.3 - - + -
214A GLU 4.6 5.4 - - - +
216A ILE* 3.9 30.1 - - + +
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Residues in contact with PHE 147 (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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33A ILE* 4.9 0.7 - - + -
105A SER* 4.0 8.5 - - - -
107A HIS* 3.3 34.8 - - + -
109A VAL* 3.7 28.9 - - + -
114A TYR* 3.6 39.7 - + + -
116A ALA 3.8 2.2 - - - -
117A GLU* 3.5 20.4 - - - -
145A GLY 6.4 0.2 - - - -
146A ILE* 1.3 76.3 - - - +
148A LEU* 1.3 61.0 + - - +
192A TRP* 4.4 2.7 - + - -
211A VAL* 3.4 33.0 - - + -
212A LEU 3.8 15.4 + - - -
213A LYS 4.9 2.0 - - - -
214A GLU 5.2 0.6 + - - -
215A PRO* 3.4 14.5 - - + +
216A ILE* 2.9 29.2 + - - +
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Residues in contact with LEU 148 (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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95A PHE* 3.8 24.9 - - + -
114A TYR* 3.5 5.3 - - - +
115A ALA* 3.1 27.0 + - + +
116A ALA* 3.1 28.1 + - + +
117A GLU* 4.4 2.2 - - - -
118A LEU* 3.9 21.3 - - + +
146A ILE 3.5 18.2 - - - +
147A PHE* 1.3 75.9 - - - +
149A LYS* 1.3 60.0 + - - +
157A LEU* 4.7 2.7 - - + -
216A ILE* 3.4 28.0 - - + +
218A VAL* 3.8 30.1 - - + -
223A VAL* 5.9 0.4 - - + -
226A PHE* 4.6 8.5 - - + -
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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