Contacts of the strand formed by residues 49 - 57 (chain E) in PDB entry 4QRR
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 GLY 49 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D PHE* 5.4 6.3 - - - -
123D GLY 5.1 1.3 - - - -
124D GLN* 4.0 15.4 + - - +
43E GLN 3.0 15.8 - - - +
44E GLN* 3.4 17.8 - - - -
45E THR* 2.8 18.3 + - - -
46E PRO* 5.8 0.2 - - - -
47E GLY 3.8 1.8 - - - +
48E GLN* 1.3 76.0 - - - +
50E LEU* 1.3 62.7 + - - -
51E GLN* 3.4 1.2 + - - +
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Residues in contact with LEU 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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50D MET* 3.8 27.8 - - + -
103D PHE* 3.9 26.9 - - + -
120D LEU 5.5 0.9 - - - +
122D PHE* 4.0 38.2 + - + +
123D GLY 5.1 2.2 + - - -
124D GLN* 5.3 0.2 - - - +
42E TYR* 4.4 14.4 - - + -
43E GLN 3.6 4.3 - - - -
44E GLN* 3.9 20.6 - - + +
48E GLN 5.0 0.7 - - - +
49E GLY* 1.3 69.0 - - - -
51E GLN* 1.3 64.4 + - - +
52E PHE 4.2 0.7 + - - -
103E LEU* 3.9 21.8 - - + -
118E PHE* 4.2 23.8 - - + -
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Residues in contact with GLN 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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42E TYR* 4.2 2.0 - - - -
43E GLN* 2.8 42.2 + - + +
48E GLN* 4.1 43.0 + - + +
49E GLY 4.3 2.5 - - - +
50E LEU* 1.3 74.9 - - - +
52E PHE* 1.3 64.8 + - - +
53E LEU 3.6 0.2 + - - -
70E ASN* 6.3 1.4 - - - +
71E PHE* 3.7 29.5 - - + -
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Residues in contact with PHE 52 (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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117D TYR 3.8 1.1 - - - -
118D GLY 3.3 23.6 - - - -
119D LYS* 3.5 39.9 - - + +
120D LEU 5.6 0.2 - - - +
40E SER* 4.4 3.1 - - - -
41E TRP 3.9 5.2 - - - -
42E TYR* 3.8 24.5 - + + -
50E LEU 4.2 0.6 + - - -
51E GLN* 1.3 70.6 + - - +
53E LEU* 1.3 60.9 + - - +
54E PHE* 3.5 33.0 - - - -
55E GLU* 3.6 10.5 - - + -
67E ASN* 3.4 33.0 - - - -
68E LYS 3.8 13.5 - - - -
69E GLY* 3.7 24.2 - - - -
70E ASN 4.4 0.9 + - - -
71E PHE* 3.3 17.2 - - - -
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Residues in contact with LEU 53 (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 TRP* 2.8 17.6 + - + +
42E TYR 3.7 33.2 - - - +
43E GLN* 4.0 2.5 - - + +
52E PHE* 1.3 72.3 - - - +
54E PHE* 1.4 75.7 + - + +
68E LYS* 3.8 2.9 - - - +
69E GLY* 2.7 29.5 + - - -
71E PHE* 3.7 32.2 - - + +
76E PHE* 3.6 38.6 - - + -
89E MET* 3.9 25.4 - - + -
102E TYR* 4.0 9.2 - - + -
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Residues in contact with PHE 54 (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 VAL 4.2 0.3 - - - +
40E SER* 3.6 1.4 - - - -
41E TRP* 3.0 55.6 + + + -
52E PHE* 3.5 11.9 - - - -
53E LEU* 1.4 98.7 - - + +
55E GLU* 1.3 59.5 + - - +
56E TYR* 3.5 16.8 - + + -
61E GLN* 3.4 28.5 - - - +
67E ASN 3.4 9.6 - - - +
68E LYS* 4.2 6.1 - - + -
71E PHE* 6.2 0.7 - - + -
76E PHE* 3.6 33.4 - - + -
77E SER 3.2 20.0 - - - -
78E GLY* 3.9 8.3 - - - -
89E MET* 3.8 24.0 - - + -
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Residues in contact with GLU 55 (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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117D TYR* 3.4 30.1 - - - +
118D GLY* 3.7 3.8 - - - -
31E SER* 2.7 25.4 + - - +
39E VAL 3.4 3.8 - - - +
40E SER* 3.5 19.7 - - - +
52E PHE* 3.7 8.1 - - + -
54E PHE* 1.3 74.3 - - - +
56E TYR* 1.3 80.2 + - - +
57E PHE* 3.6 4.5 - - - +
61E GLN* 3.4 6.9 - - - +
66E ARG* 3.1 64.6 + - - +
67E ASN* 2.8 12.7 + - + +
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Residues in contact with TYR 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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30E ARG 3.9 0.7 - - - +
31E SER* 3.5 1.9 - - - -
39E VAL* 2.8 40.8 + - + +
41E TRP* 4.7 4.0 - + - -
54E PHE* 3.5 30.3 - + - -
55E GLU* 1.3 82.7 - - - +
57E PHE* 1.3 56.5 + - - +
59E GLU 4.5 2.7 - - - -
60E THR* 3.4 17.3 - - - -
61E GLN* 2.8 43.5 + - + +
78E GLY* 2.9 40.6 + - - -
79E ARG* 4.0 10.1 - - - +
80E GLN* 3.4 38.2 - - + +
87E SER* 4.7 4.9 - - - +
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Residues in contact with PHE 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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76A GLU* 3.3 32.5 - - + -
30E ARG* 3.5 61.9 - - + -
31E SER* 3.9 5.8 - - - -
55E GLU* 3.6 5.5 + - - +
56E TYR* 1.3 73.4 - - - +
58E SER* 1.4 72.8 - - - +
60E THR* 2.9 26.6 + - - +
66E ARG* 3.4 46.8 - - - +
80E GLN* 3.3 3.8 + - - -
109E GLU* 3.7 28.0 - - + -
8P HIS* 4.0 12.8 - + - -
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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