Contacts of the strand formed by residues 41 - 53 (chain A) in PDB entry 3WJG
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 ILE 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLU* 3.8 4.8 - - - +
38A TYR* 2.7 57.6 + - + +
39A PRO 3.3 1.6 + - - -
40A THR* 1.3 90.8 - - + +
42A PRO* 1.3 83.0 - - + +
43A SER 3.5 1.0 + - - -
44A PHE* 3.8 24.7 - - + -
148A TRP* 6.2 4.9 - - + -
158A LEU* 4.5 9.9 - - + -
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Residues in contact with PRO 42 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLU* 5.3 0.4 - - + -
40A THR 4.0 5.6 - - - +
41A ILE* 1.3 101.0 - - + +
43A SER* 1.3 70.8 + - - +
44A PHE* 3.5 5.7 + - - +
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Residues in contact with SER 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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35A GLU* 3.7 21.2 + - - -
36A GLY 3.1 13.7 - - - -
37A GLU* 3.9 21.3 + - - +
41A ILE 3.5 1.6 + - - -
42A PRO* 1.3 80.1 - - - +
44A PHE* 1.3 60.5 + - - +
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Residues in contact with PHE 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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35A GLU* 3.2 7.7 - - - +
36A GLY* 2.8 56.5 + - - -
37A GLU 4.2 0.4 - - - -
41A ILE* 3.8 19.7 - - + -
42A PRO 3.6 12.6 - - - +
43A SER* 1.3 74.5 - - - +
45A ARG* 1.3 67.8 + - - +
46A TYR* 3.8 26.5 - + + -
75A LEU* 6.1 2.9 - - + -
158A LEU* 5.1 6.1 - - + -
159A LEU* 3.9 12.8 - - + -
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Residues in contact with ARG 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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33A GLN* 4.9 9.1 + - - -
34A GLY 3.3 12.8 + - - +
35A GLU* 2.8 40.2 + - + +
44A PHE* 1.3 84.4 - - - +
46A TYR* 1.3 65.7 + - - +
67A TRP 4.8 0.3 - - - +
68A LYS* 5.3 1.2 - - - -
69A LEU* 3.7 27.0 + - + +
75A LEU* 4.8 5.0 - - - +
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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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33A GLN* 3.2 6.6 - - - +
34A GLY* 2.8 43.1 + - - -
35A GLU 3.5 22.9 - - - -
36A GLY 4.0 1.1 - - - -
44A PHE* 3.8 17.7 - + + -
45A ARG* 1.3 80.3 - - - +
47A GLY* 1.3 72.3 + - - +
48A GLU* 3.4 21.1 - - - -
66A THR* 3.6 17.5 - - + -
67A TRP 3.4 12.6 - - - +
69A LEU* 3.7 9.3 - - - +
75A LEU* 4.0 14.4 - - + -
144A TYR* 2.8 18.5 + - - -
159A LEU* 3.4 33.2 - - + +
160A LYS 3.8 9.5 + - - -
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Residues in contact with GLY 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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32A GLY 3.5 9.9 - - - -
46A TYR* 1.3 74.5 - - - +
48A GLU* 1.3 61.0 - - - +
66A THR* 3.0 10.4 - - - -
67A TRP* 2.8 56.2 + - - -
69A LEU* 3.4 11.7 - - - +
401A GOL 4.0 0.2 - - - -
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Residues in contact with GLU 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 ARG* 3.3 5.5 - - - +
32A GLY 2.9 37.7 + - - +
33A GLN* 5.0 2.0 - - - +
46A TYR* 3.4 12.7 - - + -
47A GLY* 1.3 75.6 - - - +
49A GLU* 1.3 60.6 + - - +
50A ILE* 3.5 9.2 - - - +
62A TYR* 4.7 1.2 + - - -
64A GLN* 2.9 35.6 - - + +
65A LYS 3.3 11.0 - - - +
66A THR* 4.0 3.4 - - + -
67A TRP* 3.3 7.9 - - - -
144A TYR* 2.4 46.1 + - - -
161A ALA* 3.5 5.1 - - + +
163A LEU* 3.6 13.4 - - + +
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Residues in contact with GLU 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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29A THR* 3.9 19.5 - - + +
30A TRP 3.2 13.0 - - - +
31A ARG* 2.9 38.3 + - - +
48A GLU* 1.3 74.8 - - - +
50A ILE* 1.3 66.6 + - - +
51A ARG* 5.9 1.5 - - + +
63A THR 4.0 0.2 - - - +
64A GLN* 3.2 6.8 - - - +
65A LYS* 2.9 59.2 + - + +
67A TRP* 3.4 14.1 - - + -
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Residues in contact with ILE 50 (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 THR* 3.4 2.4 - - - +
30A TRP* 2.8 42.4 + - + -
48A GLU* 3.5 24.0 - - - +
49A GLU* 1.3 81.3 - - - +
51A ARG* 1.3 63.2 + - - +
52A PHE* 3.5 32.1 - - + -
62A TYR* 3.7 27.6 - - + +
63A THR 3.3 3.4 - - - -
64A GLN* 3.7 9.0 - - + -
135A PHE* 4.9 4.9 - - + -
142A LEU* 4.3 12.3 - - + -
144A TYR* 4.4 9.2 - - + -
163A LEU* 4.0 21.7 - - + +
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Residues in contact with ARG 51 (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 GLY* 3.4 12.2 - - - +
29A THR* 3.8 19.8 + - + +
49A GLU* 5.9 1.6 - - + +
50A ILE* 1.3 75.0 - - - +
52A PHE* 1.3 70.2 + - - +
53A SER* 3.6 31.9 + - - -
61A ALA 3.5 1.0 - - - +
62A TYR* 3.4 4.3 - - - -
63A THR* 2.8 50.2 + - - +
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Residues in contact with PHE 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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26A LEU* 3.4 58.1 - - + +
27A LEU* 3.6 5.9 - - - +
28A GLY* 3.0 30.5 + - - +
30A TRP* 3.9 5.8 - - - -
50A ILE* 3.5 20.4 - - + -
51A ARG* 1.3 73.5 + - - +
53A SER* 1.3 62.2 + - - +
60A ILE* 3.8 23.6 - - + -
61A ALA 3.2 8.7 - - - -
62A TYR* 3.6 30.3 - + + -
82A PHE* 3.7 32.1 - + - -
135A PHE* 4.8 7.0 - + - -
142A LEU* 4.0 15.3 - - + -
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Residues in contact with SER 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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27A LEU* 4.0 6.7 - - - -
51A ARG* 3.6 40.6 + - - +
52A PHE* 1.3 75.4 - - - +
54A HIS* 1.3 66.5 + - - +
60A ILE* 3.4 4.5 - - - +
61A ALA* 2.8 45.2 + - - +
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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