Contacts of the strand formed by residues 52 - 61 (chain A) in PDB entry 4ES7
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 GLU 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TYR* 5.2 1.7 + - - -
46A GLU* 4.1 1.9 - - - -
47A GLY* 3.0 24.2 + - - -
48A ALA* 3.7 24.5 + - - +
49A THR* 3.2 28.1 + - - +
50A GLU 4.5 2.6 - - - -
51A ALA* 1.3 84.9 - - + +
53A ILE* 1.3 67.3 + - - +
71A ALA* 3.3 25.3 - - + +
72A TYR 3.3 10.8 - - - +
73A GLU* 4.7 13.7 - - + +
74A LYS* 4.5 3.2 + - - -
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.7 22.0 - - + -
14A ILE* 5.8 0.2 - - + -
15A TYR* 4.1 15.9 - - + +
44A LEU* 4.4 10.3 - - + -
45A GLY 3.4 13.7 - - - +
47A GLY* 4.2 2.0 - - - -
52A GLU* 1.3 78.3 - - - +
54A SER* 1.3 70.5 + - - +
55A MET* 3.5 17.2 + - - +
71A ALA* 3.6 2.3 - - - -
72A TYR* 2.9 42.8 + - + +
74A LYS* 4.4 8.7 - - + +
81A PHE* 3.5 46.0 - - + -
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL 3.5 1.6 - - - +
44A LEU* 3.4 6.9 - - - -
45A GLY* 2.9 35.2 + - - -
46A GLU 3.5 20.0 - - - -
47A GLY* 3.8 7.7 - - - +
53A ILE* 1.3 73.0 - - - +
55A MET* 1.3 59.9 + - - +
56A THR* 4.1 11.7 + - - -
69A SER* 5.0 3.5 + - - -
70A GLY 3.8 5.6 + - - -
71A ALA* 4.9 2.5 - - - +
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Residues in contact with MET 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.0 31.0 - - + -
43A VAL 3.7 2.7 - - - -
44A LEU* 3.6 27.6 - - + -
53A ILE* 3.9 17.0 - - - +
54A SER* 1.3 71.8 + - - +
56A THR* 1.3 64.2 + - - +
57A SER 4.3 0.4 - - - -
68A THR 4.7 0.2 - - - -
69A SER* 3.3 5.4 + - - -
70A GLY 2.9 38.4 + - - +
72A TYR* 3.3 55.9 - - + +
81A PHE* 6.1 4.5 - - + -
107A PHE* 5.9 6.5 - - + -
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 3.7 1.0 + - - +
42A LEU* 3.3 6.0 - - - +
43A VAL* 2.8 51.2 + - + +
54A SER* 4.1 9.9 + - - -
55A MET* 1.3 78.0 + - - +
57A SER* 1.3 60.6 + - - +
58A THR* 5.2 2.2 - - - +
67A GLU* 3.6 39.9 - - + +
68A THR 3.5 3.8 - - - +
69A SER* 4.0 9.4 + - - +
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A SER* 4.3 13.2 + - - -
41A THR 3.1 10.5 + - - -
42A LEU* 4.4 12.5 - - - +
55A MET 4.3 0.4 - - - -
56A THR* 1.3 73.7 - - - +
58A THR* 1.3 63.5 + - - +
59A ARG* 5.4 3.5 - - - +
66A GLU 3.6 1.0 - - - +
67A GLU* 3.3 4.3 - - - +
68A THR* 2.8 51.4 + - - +
123A LYS* 6.0 0.2 + - - -
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Residues in contact with THR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A SER* 3.3 2.9 - - - -
41A THR* 2.9 50.4 + - + +
56A THR* 5.2 2.6 - - - +
57A SER* 1.3 77.2 + - - +
59A ARG* 1.3 66.0 + - - +
65A CYS* 3.7 2.7 - - - -
66A GLU 3.3 4.2 + - - -
67A GLU* 4.1 8.5 + - - +
162A CYS* 3.1 45.5 - - - +
164A PRO* 3.8 21.5 - - + +
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.6 18.2 - - - +
37A MET* 4.6 36.5 - - - +
38A THR* 5.0 8.5 - - - +
39A VAL 5.2 1.6 - - - +
40A SER* 3.5 22.9 - - - +
57A SER* 5.4 3.1 - - - +
58A THR* 1.3 79.3 - - - +
60A TRP* 1.3 76.7 + - - +
61A ARG* 3.5 31.7 + - + +
66A GLU* 2.8 38.3 + - + +
68A THR* 5.5 4.8 + - - -
162A CYS* 4.1 6.7 - - - -
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Residues in contact with TRP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG 5.4 3.3 - - - +
37A MET* 6.1 0.3 - - - -
38A THR* 4.4 23.0 + - - +
39A VAL 5.5 1.5 + - - -
59A ARG* 1.3 85.3 + - - +
61A ARG* 1.3 61.9 + - - +
62A LYS 5.1 4.9 - - - +
63A GLY 4.1 14.1 - - - -
64A VAL* 3.4 23.1 - - - -
65A CYS* 3.8 14.6 - - + -
159A ARG* 3.5 28.5 + - + -
160A GLY 3.7 20.0 + - - +
161A GLU 4.4 4.3 - - - -
162A CYS* 3.4 33.0 - - + +
166A GLU* 5.7 2.7 - - - -
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 5.9 4.8 - - - -
59A ARG* 3.5 30.1 + - - +
60A TRP* 1.3 75.3 - - - +
62A LYS* 1.3 101.4 + - + +
64A VAL* 2.9 27.5 + - - +
66A GLU* 3.7 33.1 + - + +
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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