Contacts of the strand formed by residues 55 - 61 (chain E) in PDB entry 2C2V
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 THR 55 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E VAL* 4.2 15.3 - - + -
43E ILE 3.6 5.8 - - - +
44E ALA* 5.1 4.0 - - + -
53E GLY 4.7 2.5 - - - +
54E GLY* 1.3 81.7 - - - +
56E PHE* 1.3 60.4 + - - +
57E LYS* 4.1 0.4 - - - -
152E ALA* 2.8 34.1 + - - +
153E MET* 4.9 0.9 - - - -
154E ASN 5.3 0.5 + - - -
155E ASN* 3.3 29.5 + - - -
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Residues in contact with PHE 56 (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 VAL* 3.5 3.6 - - - +
43E ILE* 3.0 41.2 + - + +
45E GLY* 3.8 15.7 - - - -
51E PHE* 3.5 31.2 - + + -
54E GLY 4.1 6.7 - - - -
55E THR* 1.3 72.2 - - - +
57E LYS* 1.3 64.4 + - - +
58E LEU* 3.2 3.4 - - + +
75E PHE* 4.3 17.7 - + + -
77E THR* 3.8 21.1 - - + -
78E LYS 4.6 3.6 - - - -
79E ILE* 3.4 37.2 - - + -
116E LEU* 4.3 10.3 - - + -
148E THR* 3.8 15.3 - - + -
152E ALA* 3.6 18.6 - - + -
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Residues in contact with LYS 57 (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 VAL 3.7 9.6 - - - +
42E VAL* 4.4 11.9 - - + +
55E THR 4.1 0.6 - - - +
56E PHE* 1.3 71.5 - - - +
58E LEU* 1.4 65.2 + - - +
75E PHE* 4.0 1.6 - - - +
76E MET* 2.9 46.0 + - + -
77E THR* 3.3 13.1 + - - +
155E ASN* 3.9 18.3 - - - +
156E ILE* 3.4 35.2 + - - +
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Residues in contact with LEU 58 (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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40E HIS* 4.3 1.4 - - - -
41E VAL* 3.2 36.8 + - + +
43E ILE* 4.0 29.6 - - + -
56E PHE* 3.2 18.8 - - + +
57E LYS* 1.4 75.5 - - - +
59E GLU* 1.3 67.6 + - - +
73E VAL* 4.8 3.4 - - + -
74E ARG 3.5 10.8 - - - +
75E PHE* 3.8 44.9 - - + +
76E MET* 4.1 4.2 - - - +
90E ILE* 4.5 1.8 - - + -
112E ILE* 4.5 18.2 - - + -
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Residues in contact with GLU 59 (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 TYR* 1.9 52.2 + - + +
39E PHE 3.7 8.1 - - - +
40E HIS* 5.5 1.6 - - - +
41E VAL 4.6 0.4 - - - +
58E LEU* 1.3 76.7 - - - +
60E LEU* 1.4 57.7 - - - +
73E VAL* 3.5 2.8 - - - +
74E ARG* 3.0 40.1 + - - +
76E MET* 3.9 16.8 - - + -
41F ASN* 3.1 42.6 + - - +
42F PHE* 3.7 21.1 - - + -
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Residues in contact with LEU 60 (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 TYR* 3.4 4.0 - - - -
39E PHE* 2.7 59.3 + - + +
41E VAL* 4.3 8.3 - - + -
58E LEU* 6.1 0.2 - - + -
59E GLU* 1.4 73.7 - - - +
61E PHE* 1.3 71.7 + - - +
62E LEU* 4.4 8.7 - - + -
71E PRO* 4.3 12.6 - - + -
72E LYS 3.4 0.9 - - - +
73E VAL* 3.2 26.2 - - + -
105E ILE* 4.2 18.6 - - + -
108E VAL* 4.5 13.7 - - + -
109E LEU* 3.7 29.4 - - + -
112E ILE* 6.0 0.2 - - + -
42F PHE* 4.4 1.7 - - - -
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Residues in contact with PHE 61 (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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35E ASN* 4.7 2.7 - - - -
37E ARG* 3.3 36.8 - - + -
38E TYR* 4.2 3.6 - - + -
60E LEU* 1.3 77.3 - - - +
62E LEU* 1.4 81.2 + - - +
63E PRO* 3.6 12.7 - - + +
71E PRO* 3.3 5.4 - - - +
72E LYS* 2.6 56.5 + - + +
36F VAL* 4.8 12.1 - - + -
37F LYS 3.6 18.8 - - - -
38F VAL* 3.8 15.0 - - + -
39F PRO* 3.5 35.4 - - + -
42F PHE* 3.8 20.6 - + + -
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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