Contacts of the strand formed by residues 40 - 49 (chain A) in PDB entry 2F4W
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.0 26.7 + - + +
38A PRO 3.3 1.2 - - - -
39A SER* 1.3 84.3 + - - +
41A ILE* 1.3 64.0 + - - +
42A LEU* 3.0 29.3 + - - +
43A GLU* 3.2 39.6 + - + +
66A ILE* 6.3 0.6 - - - +
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Residues in contact with ILE 41 (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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14A THR* 3.7 35.9 - - + +
17A LEU* 3.5 16.4 - - + +
18A LYS* 3.5 48.2 - - + +
21A TYR* 6.0 1.6 - - + -
36A PRO* 4.4 14.4 - - + -
37A LEU 3.9 4.4 + - - -
40A ASN* 1.3 73.0 + - - +
42A LEU* 1.3 64.8 + - + +
43A GLU 3.2 0.2 - - - -
44A TRP* 2.9 36.0 + - + +
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Residues in contact with LEU 42 (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 ALA* 3.8 21.3 - - + -
14A THR* 4.5 4.0 - - + -
17A LEU* 3.7 24.2 - - + -
40A ASN* 3.0 18.1 + - - +
41A ILE* 1.3 82.2 - - + +
43A GLU* 1.3 58.5 + - - +
66A ILE* 3.4 4.8 - - + +
67A PHE* 2.8 57.3 + - + +
68A PRO 4.4 1.3 - - - +
69A ARG* 3.6 45.1 - - + +
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Residues in contact with GLU 43 (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 PRO* 3.6 1.6 - - - +
37A LEU* 2.9 49.6 + - + +
40A ASN* 3.2 23.4 + - - +
41A ILE 3.2 0.2 - - - -
42A LEU* 1.3 79.6 - - - +
44A TRP* 1.3 62.4 + - - +
45A HIS* 2.9 22.6 + - + -
64A LYS* 2.9 33.9 + - + +
65A LEU 3.4 8.7 - - - +
66A ILE* 4.1 16.1 - - + +
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Residues in contact with TRP 44 (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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17A LEU* 3.4 33.0 - - + +
20A ASP 4.1 3.8 - - - -
21A TYR* 3.6 46.0 - + + -
24A ILE* 4.3 7.9 - - + -
34A ALA* 3.9 20.9 - - + -
35A GLU 3.5 4.0 - - - +
36A PRO* 3.9 25.5 - - + +
41A ILE* 2.9 32.0 + - + +
43A GLU* 1.3 76.0 - - - +
45A HIS* 1.3 65.4 + - - +
64A LYS* 3.1 4.9 - - - +
65A LEU* 2.7 45.0 + - + +
67A PHE* 3.5 21.5 - + + -
111A VAL* 3.7 34.3 - - + -
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Residues in contact with HIS 45 (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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34A ALA* 3.5 3.8 - - - +
35A GLU 2.9 33.0 + - - +
37A LEU* 3.5 25.8 - - + +
43A GLU* 2.9 26.6 + - + -
44A TRP* 1.3 80.4 - - - +
46A TYR* 1.3 62.2 + - - +
62A HIS* 2.9 30.3 + + - +
63A GLY 3.3 8.3 + - - +
64A LYS* 4.1 9.2 - - + +
81A ILE* 4.1 13.9 - - + +
155A VAL* 4.0 16.6 - - + +
159A LEU* 3.6 21.5 - - + +
160A PHE* 3.4 7.1 - - + -
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Residues in contact with TYR 46 (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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32A ILE* 4.8 1.8 - - + -
33A CYS 3.2 12.3 - - - +
34A ALA* 4.4 1.1 - - + -
45A HIS* 1.3 76.3 - - - +
47A VAL* 1.3 68.1 + - - +
48A VAL* 3.9 23.6 - - + -
61A TYR 4.1 4.5 - - - -
62A HIS* 3.3 8.5 - - - -
63A GLY* 2.9 48.5 + - - +
64A LYS* 3.3 30.1 - - - -
65A LEU* 4.1 13.9 - - + -
78A ILE* 4.2 1.4 - - + +
79A TYR 2.7 22.1 + - - -
80A MET* 3.7 15.0 - - + +
93A LEU* 5.1 0.3 - - - +
115A LEU* 3.7 31.2 - - + -
118A LEU* 3.4 27.3 - - + +
160A PHE* 3.7 2.7 - - - -
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Residues in contact with VAL 47 (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 TYR 3.5 1.4 - - - +
32A ILE* 3.4 5.9 - - - +
33A CYS* 2.9 34.8 + - + +
46A TYR* 1.3 75.1 - - - +
48A VAL* 1.3 75.1 + - - +
49A ARG 4.1 0.6 + - - +
60A TYR* 4.4 7.9 - - + -
61A TYR 3.4 15.3 - - - +
156A PHE* 3.9 22.7 - - + -
160A PHE* 3.5 44.2 - - + -
163A VAL* 4.3 19.7 - - + -
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Residues in contact with VAL 48 (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 TYR 3.4 6.5 - - - +
32A ILE* 3.4 22.4 - - + -
46A TYR* 3.9 22.2 - - + -
47A VAL* 1.3 75.3 - - - +
49A ARG* 1.3 70.4 + - - +
50A GLY* 4.5 1.1 - - - +
60A TYR* 3.5 2.1 - - - -
61A TYR* 2.6 53.7 + - + +
80A MET* 5.0 6.1 - - + -
115A LEU* 5.6 0.7 - - + +
118A LEU* 5.1 6.3 - - + -
119A LEU* 3.5 37.0 - - + -
122A MET* 4.9 9.0 - - - -
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Residues in contact with ARG 49 (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 TYR* 2.8 74.4 + - + +
47A VAL* 4.1 1.6 + - - +
48A VAL* 1.3 76.2 - - - +
50A GLY* 1.3 73.4 + - - +
51A PRO* 3.2 5.7 - - - +
52A GLU* 5.2 7.7 + - - -
58A GLY* 6.0 1.6 - - - +
59A GLY 3.5 5.2 - - - +
60A TYR* 3.4 28.5 - - + -
166A GLU* 3.3 30.3 + - - -
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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