Contacts of the strand formed by residues 44 - 51 (chain E) in PDB entry 4NQC
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 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E TYR* 3.3 4.9 - - - -
36E ARG* 3.0 57.3 + - + +
38E ASP* 2.8 30.7 + - - -
41E MET* 3.5 27.0 - - - +
42E GLY 3.7 8.9 + - - +
43E LEU* 1.3 77.0 - - - +
45E LEU* 1.4 62.2 + - - +
46E ILE 3.6 0.7 + - - -
59E GLU* 3.4 33.4 + - - +
60E VAL* 3.6 33.9 - - + +
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Residues in contact with LEU 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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96D GLN* 6.1 5.4 - - + -
33E TYR* 3.9 27.4 - - + -
34E TRP 3.4 17.0 - - - +
35E TYR* 3.7 27.3 - - + +
43E LEU 4.3 0.2 + - - -
44E ARG* 1.4 71.6 - - - +
46E ILE* 1.3 57.6 + - - +
47E TYR 3.5 14.8 - - - +
48E TYR* 3.8 29.6 - - + -
58E GLY* 4.1 13.2 - - - -
59E GLU* 2.7 34.3 + - + +
60E VAL* 3.0 8.7 + - - +
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Residues in contact with ILE 46 (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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34E TRP* 2.8 18.7 + - + +
35E TYR 4.0 11.9 - - - -
36E ARG* 4.0 4.7 - - + +
44E ARG 4.1 5.8 - - - +
45E LEU* 1.3 71.9 - - - +
47E TYR* 1.4 69.3 + - + +
58E GLY* 2.7 24.6 + - - -
60E VAL* 3.5 26.0 - - + +
61E PRO* 3.6 9.5 - - - +
64E TYR* 3.5 41.7 - - + -
76E LEU* 4.0 16.4 - - + -
89E TYR* 3.6 37.9 - - + -
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Residues in contact with TYR 47 (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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34E TRP* 3.1 25.1 + - + +
45E LEU* 3.5 6.1 - - - +
46E ILE* 1.4 94.8 - - + +
48E TYR* 1.3 64.5 + - - +
55E THR* 5.4 1.3 - - - -
56E ASP* 3.3 24.9 - - - -
57E LYS* 3.6 16.4 - - + +
58E GLY 3.9 2.0 - - - +
61E PRO* 3.4 36.7 + - + +
64E TYR* 3.5 24.6 + - + -
65E ASN* 4.0 7.2 - - + +
66E VAL* 3.4 46.7 - - + -
74E PHE* 3.9 2.6 - - - -
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Residues in contact with TYR 48 (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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61C ARG* 2.9 42.5 + - - -
64C GLN* 3.3 23.0 - - + +
32E MET 3.4 12.3 - - - +
33E TYR* 3.7 26.0 - + + -
45E LEU* 3.8 22.2 - - + -
47E TYR* 1.3 76.2 - - - +
49E SER* 1.3 62.2 + - - +
50E ALA* 4.0 24.2 - - + -
55E THR* 3.3 6.9 - - - -
56E ASP* 2.9 53.9 + - + +
57E LYS 3.5 19.3 - - - -
58E GLY* 5.0 0.2 - - - -
74E PHE* 3.6 5.7 - - - -
97E THR* 5.2 1.6 - - + -
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Residues in contact with SER 49 (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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31E SER* 3.2 2.9 - - - -
32E MET 2.8 38.0 + - - +
33E TYR* 6.1 0.2 - - - -
48E TYR* 1.3 76.4 - - - +
50E ALA* 1.4 60.9 + - - +
51E SER 3.1 3.9 + - - -
54E THR 2.6 24.5 + - - -
55E THR* 4.0 1.8 - - - +
68E ARG* 2.7 36.2 + - - +
74E PHE* 3.7 22.7 - - - -
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Residues in contact with ALA 50 (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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64C GLN* 3.4 32.5 + - + +
65C LEU* 5.0 0.4 - - + -
68C GLY* 4.4 7.0 - - - +
30E ASN* 3.7 6.0 - - - +
31E SER* 2.9 20.0 + - - -
48E TYR* 4.0 17.8 - - + -
49E SER* 1.4 72.3 - - - +
51E SER* 1.3 60.3 + - - +
54E THR* 4.0 10.6 + - + +
55E THR* 5.3 0.2 - - - +
96E TRP* 5.1 1.7 - - - -
97E THR* 3.5 28.2 + - + +
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Residues in contact with SER 51 (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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67C ARG* 4.3 4.3 - - - -
68C GLY* 3.8 20.3 - - - -
71C GLN* 3.5 30.1 - - - +
30E ASN* 3.4 16.4 + - - +
49E SER* 3.1 4.6 + - - -
50E ALA* 1.3 77.9 - - - +
52E GLU* 1.3 74.1 + - - +
54E THR* 3.1 30.0 + - - +
68E ARG* 3.6 6.3 - - - -
96E TRP* 4.7 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