Contacts of the strand formed by residues 51 - 60 (chain A) in PDB entry 2F24
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 LEU 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLU* 3.5 5.4 - - - +
40A GLN* 2.8 46.6 + - - +
49A ALA* 3.3 21.7 + - + +
50A GLU* 1.3 80.1 - - - +
52A ILE* 1.3 66.2 + - - +
53A VAL* 5.5 0.2 - - + -
73A VAL* 3.9 26.0 - - + -
74A VAL 5.9 1.3 - - - +
77A ALA 5.3 0.7 - - - +
78A ARG* 3.6 53.2 - - + +
82A HIS 5.6 1.6 - - - +
84A SER* 4.3 5.5 - - - +
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Residues in contact with ILE 52 (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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37A PHE* 4.1 19.1 - - + -
38A ALA 3.4 9.4 - - - +
39A GLU* 4.9 1.8 - - + -
51A LEU* 1.3 78.3 - - - +
53A VAL* 1.3 72.7 + - - +
73A VAL* 3.8 5.0 - - - +
74A VAL* 2.9 37.0 + - + +
77A ALA* 4.5 12.6 + - + -
84A SER* 4.1 21.7 - - - +
85A MET* 4.4 2.5 - - - +
87A PRO* 3.9 31.4 - - + -
100A LEU* 4.4 5.8 - - + -
102A PHE* 3.6 34.8 - - + -
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Residues in contact with VAL 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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13A PHE* 3.6 25.6 - - + -
20A TYR* 4.0 15.3 - - + -
37A PHE* 3.3 5.1 - - - -
38A ALA 2.9 42.8 + - - +
40A GLN* 3.8 25.8 - - + +
51A LEU* 4.1 1.1 + - + -
52A ILE* 1.3 82.8 - - - +
54A LEU* 1.3 62.4 + - - +
71A GLN* 3.8 23.3 - - + +
72A GLU 3.4 7.0 - - - +
73A VAL* 4.0 17.7 - - + -
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Residues in contact with LEU 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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13A PHE* 4.6 0.9 - - - -
35A LEU* 3.7 22.9 - - + -
36A ALA 3.2 26.5 - - - +
37A PHE* 3.9 22.0 - - + -
53A VAL* 1.3 77.5 - - - +
55A ARG* 1.3 89.9 + - - +
56A ARG* 4.6 3.6 - - + +
70A ALA 4.1 1.2 - - - +
71A GLN* 3.5 2.9 - - - -
72A GLU* 2.7 41.7 + - + +
74A VAL* 3.9 13.9 - - + -
133A GLY 4.3 17.9 - - - +
136A TRP* 4.4 11.7 - - + +
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Residues in contact with ARG 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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10A GLU* 4.9 5.1 + - - -
11A SER 4.5 3.2 + - - -
12A VAL* 2.9 48.4 + - - +
13A PHE* 3.8 14.8 - - + -
36A ALA* 2.9 35.1 + - + +
54A LEU* 1.3 83.2 - - - +
56A ARG* 1.3 60.3 + - - +
68A TRP* 3.4 43.2 + - + +
69A GLN 2.8 27.4 + - - +
70A ALA* 4.5 6.3 - - - +
71A GLN* 3.7 23.7 - - + +
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Residues in contact with ARG 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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28A LEU* 4.2 8.7 - - - +
31A GLN* 5.9 1.2 - - - +
33A SER* 4.9 6.6 - - - -
34A LEU 3.5 9.6 - - - +
35A LEU* 3.7 18.4 - - + +
54A LEU* 4.3 4.4 - - + +
55A ARG* 1.3 74.0 - - - +
57A GLY* 1.3 59.9 + - - +
58A ASP* 3.9 9.9 - - - +
68A TRP* 3.6 2.6 - - - -
69A GLN* 2.7 73.1 + - + +
70A ALA 4.9 1.2 + - - -
132A HIS* 2.9 30.3 + - - +
133A GLY* 3.0 26.1 + - - -
134A ARG* 3.1 42.7 - - - +
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Residues in contact with GLY 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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33A SER* 3.2 2.9 - - - -
34A LEU* 2.7 39.4 + - - +
56A ARG* 1.3 76.6 - - - +
58A ASP* 1.3 64.7 + - - -
59A TYR 4.0 0.2 + - - -
66A VAL* 3.6 12.1 - - - +
67A GLN 3.4 10.1 - - - -
68A TRP* 3.6 16.7 - - - -
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Residues in contact with ASP 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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31A GLN 4.8 2.9 - - - +
32A GLN 4.6 0.9 - - - +
33A SER* 3.2 22.9 + - - +
56A ARG* 3.9 6.8 - - - +
57A GLY* 1.3 75.8 - - - -
59A TYR* 1.3 67.2 + - - +
60A ASP* 3.2 2.9 + - + -
66A VAL* 3.3 2.4 - - - -
67A GLN* 2.9 41.7 + - + +
69A GLN* 3.5 20.6 + - - +
134A ARG* 5.7 3.0 + - - -
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Residues in contact with TYR 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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27A TYR* 5.5 3.8 - - + -
32A GLN* 3.0 46.1 + - + +
33A SER* 4.4 0.6 - - - +
57A GLY 4.0 1.2 + - - -
58A ASP* 1.3 72.8 - - - +
60A ASP* 1.3 59.0 + - - +
61A ALA* 3.4 22.9 + - + +
64A HIS* 3.4 36.9 - - - +
65A GLN 3.8 4.7 - - - -
66A VAL* 4.3 10.4 - - + +
340A MET* 4.6 11.2 - - + -
342A THR 4.9 6.0 + - - -
344A PRO* 3.5 20.6 - - - +
349A LEU* 4.0 19.2 - - + +
366A MET* 3.8 31.2 - - + -
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Residues in contact with ASP 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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58A ASP 3.2 1.9 + - - +
59A TYR* 1.3 69.2 - - - +
61A ALA* 1.3 53.8 + - - +
62A PRO* 3.7 14.6 - - - +
63A THR* 2.6 42.5 + - - +
64A HIS* 2.6 36.3 + - - -
65A GLN 2.8 15.4 + - - +
67A GLN* 3.9 31.6 + - + +
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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