Contacts of the strand formed by residues 40 - 49 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.1 25.5 + - + +
38B PRO 3.4 0.6 + - - -
39B SER* 1.3 82.5 - - - +
41B ILE* 1.3 62.6 + - - +
42B LEU* 3.0 29.2 + - - +
43B GLU* 3.3 41.2 + - + +
66B ILE* 6.3 0.8 - - - +
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Residues in contact with ILE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 3.7 36.1 - - + +
17B LEU* 3.5 18.3 - - + +
18B LYS* 3.6 47.1 - - + +
21B TYR* 5.8 1.6 - - + -
36B PRO* 4.3 15.9 - - + -
37B LEU 3.9 4.4 + - - -
40B ASN* 1.3 73.1 + - - +
42B LEU* 1.3 61.6 + - + +
43B GLU 3.3 1.3 - - - -
44B TRP* 2.8 36.6 + - + +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA* 3.9 21.3 - - + -
14B THR* 4.6 3.4 - - + -
17B LEU* 3.6 24.0 - - + -
40B ASN* 3.0 18.1 + - - +
41B ILE* 1.3 86.3 - - + +
43B GLU* 1.3 56.8 + - - +
66B ILE* 3.4 6.0 - - + +
67B PHE* 2.7 57.4 + - + +
68B PRO 4.6 0.9 - - - +
69B ARG* 3.8 40.6 - - + +
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 3.7 1.4 - - - +
37B LEU* 3.0 51.0 + - + +
40B ASN* 3.3 22.7 + - - +
41B ILE 3.3 0.2 - - - -
42B LEU* 1.3 80.7 - - - +
44B TRP* 1.3 61.3 + - - +
45B HIS* 3.1 21.5 + - + +
64B LYS* 2.8 36.6 + - + +
65B LEU 3.4 8.3 - - - +
66B ILE* 4.2 15.0 - - + +
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Residues in contact with TRP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 3.4 35.4 - - + +
20B ASP 4.0 3.6 - - - -
21B TYR* 3.6 43.5 - + + -
24B ILE* 4.4 8.5 - - + -
34B ALA* 4.0 20.6 - - + -
35B GLU 3.4 5.2 - - - +
36B PRO* 4.0 24.7 - - + +
41B ILE* 2.8 33.6 + - + +
43B GLU* 1.3 76.2 - - - +
45B HIS* 1.3 65.1 + - - +
64B LYS* 3.2 3.6 - - - +
65B LEU* 2.8 41.1 + - + +
67B PHE* 3.5 25.1 - + + -
111B VAL* 3.8 29.6 - - + -
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Residues in contact with HIS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ALA* 3.3 4.5 - - - +
35B GLU 2.8 33.0 + - - +
37B LEU* 3.4 30.4 - - + +
43B GLU* 3.1 25.9 + - + -
44B TRP* 1.3 80.0 - - - +
46B TYR* 1.3 62.6 + - - +
62B HIS* 2.9 24.4 + + - +
63B GLY 3.4 8.6 + - - +
64B LYS* 4.3 8.3 - - + +
81B ILE* 4.0 15.3 - - + -
155B VAL* 4.1 15.3 - - + +
159B LEU* 3.7 18.2 - - + -
160B PHE* 3.6 13.0 - - + -
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Residues in contact with TYR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 4.9 2.0 - - + -
33B CYS 3.1 13.0 - - - +
34B ALA* 4.4 0.2 - - + -
45B HIS* 1.3 75.6 - - - +
47B VAL* 1.3 70.4 + - - +
48B VAL* 4.1 13.0 - - + -
61B TYR 4.1 7.6 - - - -
62B HIS* 3.3 9.2 - - - -
63B GLY* 2.9 49.3 + - - -
64B LYS* 3.3 29.2 - - - -
65B LEU* 4.1 15.0 - - + -
78B ILE* 4.3 1.1 - - + +
79B TYR 2.6 23.0 + - - -
80B MET* 3.7 18.4 - - + +
93B LEU* 5.2 0.3 - - - +
115B LEU* 3.7 31.6 - - + -
118B LEU* 3.3 29.4 - - + +
160B PHE* 3.7 1.6 - - - -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TYR 3.6 1.2 - - - +
32B ILE* 3.4 7.6 - - - +
33B CYS* 2.9 33.6 + - + +
46B TYR* 1.3 81.2 - - - +
48B VAL* 1.3 69.8 + - - +
49B ARG 4.1 0.6 + - - +
60B TYR* 4.3 9.6 - - + -
61B TYR 3.3 19.1 - - - +
62B HIS* 4.8 0.7 - - - -
156B PHE* 3.7 24.0 - - + -
160B PHE* 3.5 38.4 - - + -
163B VAL* 4.2 17.7 - - + -
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TYR 3.4 5.2 - - - +
32B ILE* 4.1 19.1 - - + -
46B TYR* 4.1 20.6 - - + -
47B VAL* 1.3 75.5 - - - +
49B ARG* 1.3 72.3 + - - +
50B GLY* 4.4 1.8 - - - +
60B TYR* 3.4 1.9 - - - -
61B TYR* 2.7 56.2 + - + +
80B MET* 4.9 5.8 - - + -
115B LEU* 5.6 1.8 - - + +
118B LEU* 5.2 6.7 - - + -
119B LEU* 3.8 31.4 - - + +
122B MET* 4.6 8.1 - - - -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TYR* 2.8 78.7 + - - +
47B VAL* 4.1 1.6 - - - +
48B VAL* 1.3 74.4 - - - +
50B GLY* 1.3 73.3 + - - +
51B PRO* 3.3 5.9 - - - +
52B GLU* 3.8 20.8 + - - -
58B GLY* 5.9 1.8 - - - +
59B GLY 3.5 7.0 - - - +
60B TYR* 3.5 29.6 - - + -
166B GLU* 3.4 26.2 + - - -
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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