Contacts of the strand formed by residues 38 - 48 (chain A) in PDB entry 3DBD
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 ARG 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.0 4.0 - - + -
30A LEU 3.6 2.9 - - - -
31A VAL* 3.8 15.9 - - + -
36A MET 4.4 0.2 + - - -
37A LYS* 1.3 73.1 - - - +
39A TYR* 1.3 58.2 + - - +
58A ASP* 3.5 6.7 + - - -
59A MET* 2.7 61.1 + - + +
60A ASP* 5.8 2.2 - - - +
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Residues in contact with TYR 39 (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 VAL* 3.5 2.0 - - - -
30A LEU* 2.6 59.7 + - + +
32A ASP* 4.9 3.8 - - - -
35A THR* 4.9 3.4 + - - +
37A LYS* 3.8 31.5 + - + +
38A ARG* 1.3 73.5 - - - +
40A MET* 1.3 62.8 + - - +
56A ILE* 4.1 24.7 - - + -
57A THR 3.3 2.9 - - - +
58A ASP* 3.4 42.0 + - + -
59A MET* 4.5 1.1 - - - -
65A PHE* 4.5 16.0 - + - -
103A HIS* 4.8 6.2 + - - +
106A PHE* 4.0 21.5 - + - -
115A VAL* 4.0 27.7 - - + +
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Residues in contact with MET 40 (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 ASP* 3.5 11.2 - - + +
29A VAL* 4.6 4.9 - - + +
39A TYR* 1.3 69.9 - - - +
41A ARG* 1.3 69.5 + - - +
42A GLY* 3.2 6.7 + - - -
56A ILE* 3.4 2.8 - - - -
57A THR* 2.8 45.3 + - - +
59A MET* 3.9 23.7 - - + +
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Residues in contact with ARG 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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25A GLU* 5.1 7.3 + - - +
26A ILE* 3.7 34.6 + - + +
27A PRO 3.6 14.3 + - - +
28A ASP* 2.8 47.0 + - - +
30A LEU* 4.7 7.2 - - + -
39A TYR 3.6 2.6 + - - -
40A MET* 1.3 74.3 - - - +
42A GLY* 1.3 74.5 + - - +
54A TYR* 3.7 47.4 - - + -
56A ILE* 4.1 12.3 - - + -
69A VAL* 6.2 0.7 - - + -
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Residues in contact with GLY 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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40A MET* 3.2 7.3 + - - -
41A ARG* 1.3 91.3 + - - +
43A ARG* 1.3 67.2 + - - -
44A PHE 3.7 0.5 + - - -
54A TYR* 3.8 4.2 - - - -
55A GLU* 2.8 20.9 + - - -
57A THR* 5.7 1.6 - - - -
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Residues in contact with ARG 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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42A GLY* 1.3 72.7 - - - +
44A PHE* 1.3 69.8 + - - +
45A LEU* 3.7 21.0 - - + +
54A TYR* 3.7 1.3 - - - -
55A GLU* 2.8 64.5 + - + +
118A ILE* 5.8 0.4 - - - +
120A ARG* 5.0 18.4 + - - +
313A 3FR 4.7 8.7 - - - +
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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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42A GLY 3.7 1.6 + - - -
43A ARG* 1.3 84.6 + - - +
45A LEU* 1.3 64.9 + - - +
46A GLY* 3.4 42.2 - - - -
47A LYS* 4.2 13.7 - - + -
52A LYS* 4.5 13.5 - - + -
53A CYS 3.7 7.0 - - - -
54A TYR* 3.5 43.2 - + + -
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Residues in contact with LEU 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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43A ARG* 3.7 40.6 - - + +
44A PHE* 1.3 79.5 - - - +
46A GLY* 1.3 60.3 + - - +
53A CYS* 3.0 31.9 + - + +
54A TYR 3.7 5.4 - - - +
55A GLU* 3.5 31.0 - - + +
66A ALA* 4.6 1.1 - - + -
118A ILE* 3.8 24.5 - - + -
313A 3FR 3.4 49.6 - - + +
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Residues in contact with GLY 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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44A PHE* 3.4 25.5 - - - -
45A LEU* 1.3 81.9 - - - +
47A LYS* 1.3 60.9 + - - -
52A LYS* 3.7 0.2 - - - -
53A CYS* 2.9 25.6 + - - +
313A 3FR 3.7 19.3 - - - -
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Residues in contact with LYS 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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44A PHE* 4.5 10.3 - - + -
46A GLY* 1.3 75.8 - - - +
48A GLY* 1.3 59.6 + - - +
49A GLY 4.0 4.8 + - - +
51A ALA 3.4 11.0 - - - +
52A LYS* 4.5 17.3 - - + -
313A 3FR 3.7 24.9 - - + -
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Residues in contact with GLY 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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47A LYS* 1.3 72.1 - - - +
49A GLY* 1.3 60.0 + - - +
50A PHE 2.9 9.1 + - - -
51A ALA* 2.8 24.1 + - - +
313A 3FR 3.7 19.1 - - - +
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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