Contacts of the strand formed by residues 39 - 45 (chain E) in PDB entry 2OCP
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 ARG 39 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E GLY* 2.9 31.6 + - - +
38E PRO* 1.3 72.7 + - - +
40E ARG* 1.3 61.1 + - - +
41E LEU* 4.5 10.1 - - + -
135E LYS* 6.3 2.5 - - - +
136E PRO* 2.9 17.6 + - - +
137E VAL* 3.5 13.6 - - + +
138E GLN 2.8 28.9 + - - +
187E HIS* 3.2 42.1 + - + -
274E VAL* 4.6 7.2 - - + +
277E LEU* 3.4 50.7 + - + -
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Residues in contact with ARG 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E PRO* 4.0 6.1 - - - +
39E ARG* 1.3 73.1 - - - +
41E LEU* 1.3 60.8 + - - +
122E GLN* 2.9 44.4 + - - +
124E GLU 5.5 1.6 + - - -
126E PHE* 3.5 26.8 - - + -
138E GLN* 2.6 39.1 + - - -
140E PHE* 3.5 10.0 - - + -
183E ARG 3.4 13.7 + - - -
185E THR* 2.8 49.8 + - - +
186E LEU* 3.7 8.9 - - + -
187E HIS* 2.6 54.9 + - + +
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ARG* 4.2 7.2 - - + +
40E ARG* 1.3 81.7 - - - +
42E SER* 1.3 56.1 + - - +
137E VAL* 3.9 17.3 - - + -
138E GLN 2.9 6.3 + - - -
139E ILE* 3.2 29.2 - - + +
140E PHE* 2.7 35.4 + - - -
186E LEU* 4.3 3.1 - - - +
188E GLY 3.1 19.5 - - - +
190E ILE* 4.4 13.2 - - + -
273E PHE* 3.6 32.3 - - + -
274E VAL* 4.2 15.0 - - + -
277E LEU* 3.7 20.6 - - + -
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Residues in contact with SER 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU* 1.3 76.5 - - - +
43E ILE* 1.3 62.4 + - - +
44E GLU* 3.1 13.9 + - - -
140E PHE* 3.1 19.5 - - - -
142E ARG 4.0 2.5 - - - -
143E SER* 3.7 14.9 - - - -
186E LEU* 3.7 7.0 - - - +
188E GLY 3.2 4.9 + - - -
189E PHE* 2.9 38.1 - - - -
190E ILE* 3.0 23.1 + - - -
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Residues in contact with ILE 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E SER* 1.3 72.1 - - - +
44E GLU* 1.3 63.1 + - - +
51E LYS* 4.1 17.1 - - + +
54E PHE* 4.0 22.2 - - + -
55E VAL* 3.5 32.5 - - + -
58E LEU* 4.3 2.0 - - + -
139E ILE* 3.7 28.0 - - + -
140E PHE 2.8 12.7 + - - +
141E GLU* 4.6 3.8 - - + -
142E ARG* 2.8 29.6 + - - +
190E ILE* 3.3 18.4 - - + +
192E LEU* 3.8 30.7 - - + -
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Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E SER* 3.1 9.2 + - - +
43E ILE* 1.3 83.1 - - - +
45E GLY* 1.3 58.1 + - - +
51E LYS* 6.0 1.1 - - - -
142E ARG* 3.5 11.0 - - - +
143E SER* 2.8 31.7 + - - -
146E SER* 2.7 32.4 + - - -
189E PHE* 3.8 24.1 - - + -
190E ILE 2.8 8.7 + - - +
191E TYR* 3.3 4.7 - - - -
192E LEU* 2.8 27.9 + - - +
226E HIS* 4.4 4.9 + - + -
229E TRP* 4.1 9.8 - - + -
230E LEU* 3.9 22.0 - - + -
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Residues in contact with GLY 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E GLU* 1.3 76.5 - - - +
46E ASN* 1.3 60.3 + - - -
49E VAL* 4.4 5.8 - - - -
51E LYS* 6.0 1.7 - - - +
142E ARG* 2.5 34.7 + - - +
191E TYR* 4.2 2.7 - - - -
192E LEU 3.8 13.2 - - - -
226E HIS* 2.8 26.6 + - - -
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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