Contacts of the strand formed by residues 35 - 44 (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 ASN 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E ASP* 2.3 39.3 + - - +
34E SER* 1.3 73.7 - - - +
36E ALA* 1.3 64.3 + - - +
37E ARG* 2.5 51.1 + - - +
38E TYR* 3.1 33.7 + - + +
61E PHE* 4.7 1.8 - - - -
37F LYS* 3.3 41.5 + - + +
39F PRO* 5.4 3.0 - - - +
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Residues in contact with ALA 36 (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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8E LEU* 4.0 25.1 - - + -
12E ILE* 4.3 8.8 - - + +
16E THR* 5.0 1.9 + - - +
31E PRO* 4.4 14.2 - - + +
32E ASP 3.8 3.0 + - - -
34E SER 4.2 0.4 - - - -
35E ASN* 1.3 73.3 - - - +
37E ARG* 1.4 62.2 + - + +
38E TYR 3.4 0.9 - - - -
39E PHE* 3.4 21.0 - - - -
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Residues in contact with ARG 37 (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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8E LEU* 3.4 37.7 - - + +
9E PRO* 3.8 17.8 - - - +
12E ILE* 3.6 26.1 - - + +
35E ASN* 2.5 24.7 - - - +
36E ALA* 1.4 74.7 - - - +
38E TYR* 1.4 54.2 + - - -
39E PHE* 3.8 9.9 - - - -
61E PHE* 3.3 13.9 - - + -
62E LEU* 3.0 54.5 + - + +
63E PRO 3.5 9.6 + - - -
64E GLU* 3.4 24.9 + - - -
66E TYR 4.6 1.2 + - - -
36F VAL* 3.5 41.0 - - - +
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Residues in contact with TYR 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E PRO* 3.7 0.5 - - - +
32E ASP* 2.7 38.7 + - + +
35E ASN* 3.1 22.1 + - + +
36E ALA 3.4 0.4 - - - -
37E ARG* 1.4 74.1 - - - +
39E PHE* 1.3 63.9 + - - +
40E HIS* 3.0 41.0 + + - -
59E GLU* 1.9 53.0 + - + +
60E LEU 3.4 7.6 - - - -
61E PHE* 4.3 4.7 - - + -
76E MET* 4.3 10.0 - - - +
39F PRO* 3.4 38.4 - - + -
41F ASN* 4.8 0.3 + - - -
42F PHE* 4.3 3.6 - + - -
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Residues in contact with PHE 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ILE* 5.4 1.3 - - + -
16E THR* 3.7 25.8 - - + -
19E LEU* 5.8 6.1 - - + -
29E ALA* 4.7 4.9 - - + -
30E GLU* 3.3 15.5 - - - +
31E PRO* 3.8 27.8 - - + -
36E ALA 3.4 22.7 - - - -
37E ARG 3.8 6.1 - - - -
38E TYR* 1.3 81.6 - - - +
40E HIS* 1.4 63.2 + - - +
41E VAL* 3.4 6.5 + - + +
59E GLU* 3.7 4.5 - - - +
60E LEU* 2.7 52.8 + - + +
62E LEU* 3.8 21.1 - - + -
105E ILE* 4.4 21.8 - - + -
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Residues in contact with HIS 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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28E LYS* 4.4 2.6 - - - +
29E ALA* 3.4 4.3 + - - -
30E GLU* 2.9 42.0 + - + +
31E PRO 5.0 0.9 - - - -
32E ASP* 3.0 31.4 + - + -
38E TYR* 3.0 34.8 + + - -
39E PHE* 1.4 68.6 - - - +
41E VAL* 1.3 60.9 + - - +
58E LEU 4.6 3.4 - - - -
59E GLU* 5.1 1.0 - - - +
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Residues in contact with VAL 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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27E ILE* 4.1 6.3 - - + -
28E LYS* 3.4 13.2 - - - +
29E ALA* 4.7 5.6 - - + -
39E PHE* 3.4 12.7 + - + +
40E HIS* 1.3 73.8 - - - +
42E VAL* 1.3 68.7 + - - +
43E ILE* 3.9 24.9 - - + -
57E LYS* 3.7 4.2 - - - +
58E LEU* 3.2 46.3 + - + +
60E LEU* 4.3 18.2 - - + -
109E LEU* 4.4 19.1 - - + -
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Residues in contact with VAL 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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26E GLY 4.0 0.6 - - - +
27E ILE* 3.6 1.6 - - - +
28E LYS* 3.1 45.6 + - + -
41E VAL* 1.3 79.7 - - - +
43E ILE* 1.3 83.3 + - - +
44E ALA* 4.4 1.3 - - + +
55E THR* 4.2 12.6 - - + -
56E PHE 3.5 17.5 - - - +
57E LYS* 4.7 15.7 - - + -
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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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26E GLY 3.9 1.8 - - - +
27E ILE* 3.9 28.7 - - + -
41E VAL* 3.9 14.6 - - + -
42E VAL* 1.3 85.9 - - - +
44E ALA* 1.3 78.4 + - - +
45E GLY 3.3 1.0 + - - -
55E THR* 3.6 0.9 - - - -
56E PHE* 3.0 37.6 + - + +
58E LEU* 4.0 17.3 - - + -
75E PHE* 5.6 1.8 - - + -
109E LEU* 5.0 3.4 - - + +
112E ILE* 3.9 29.8 - - + -
113E GLN* 4.2 17.0 - - + +
116E LEU* 4.5 11.9 - - + -
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Residues in contact with ALA 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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26E GLY* 3.1 27.0 + - - +
42E VAL* 4.4 2.4 - - + +
43E ILE* 1.3 86.1 - - - +
45E GLY* 1.3 62.6 + - - +
46E PRO* 2.6 19.8 - - - +
54E GLY 3.8 4.7 - - - +
55E THR* 4.8 4.9 - - + +
56E PHE* 4.6 0.4 - - - -
113E GLN* 5.3 0.5 - - - +
116E LEU* 4.3 0.2 - - - +
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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