Contacts of the strand formed by residues 49 - 57 (chain D) in PDB entry 3B13
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 LYS 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D GLN* 5.0 4.7 - - - +
45D MET* 3.3 3.8 - - - +
46D VAL* 2.9 34.8 + - - +
47D ASP* 3.8 8.7 - - + +
48D GLY* 1.3 83.0 - - - +
50D PRO* 1.3 70.5 - - + +
51D VAL* 3.8 6.3 + - + +
177D LEU* 4.2 30.3 - - + -
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Residues in contact with PRO 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368C TYR* 3.5 33.2 - - + +
1D MET* 3.8 20.6 - - + -
2D GLN* 3.3 17.7 + - - +
44D VAL 3.5 7.0 - - - +
45D MET* 3.9 13.0 - - + -
48D GLY 3.8 6.7 - - - +
49D LYS* 1.3 82.3 - - + +
51D VAL* 1.3 68.4 + - - +
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 4.1 6.9 - - - +
2D GLN* 3.1 19.1 - - + +
4D ILE* 4.1 13.2 - - + -
42D ALA 3.6 0.5 - - - +
43D ASN* 3.4 4.0 - - - +
44D VAL* 2.8 56.7 + - + +
46D VAL* 5.5 0.4 - - + -
49D LYS 3.8 11.0 - - - +
50D PRO* 1.3 81.4 - - - +
52D ASN* 1.3 59.5 + - - +
53D LEU* 4.2 8.7 - - + +
173D ILE* 3.6 34.8 - - + -
177D LEU* 4.5 11.7 - - + -
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Residues in contact with ASN 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1526C PRO* 4.1 21.7 - - - +
1D MET* 4.1 14.4 - - + -
2D GLN 3.0 8.7 + - - +
3D ALA* 3.5 10.1 - - + +
4D ILE 2.9 27.2 + - - +
41D SER* 3.3 24.7 + - - -
42D ALA 3.3 5.7 + - - -
43D ASN* 2.9 27.8 + - - +
51D VAL* 1.3 71.7 - - - +
53D LEU* 1.3 60.9 + - - +
54D GLY* 3.7 4.2 + - - -
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.4 34.8 - - + +
6D CYS* 3.9 17.9 - - + -
23D TYR* 4.3 10.3 - - + +
41D SER* 3.4 3.3 + - - -
42D ALA* 2.9 42.2 + - + +
44D VAL* 5.0 1.1 - - + -
51D VAL* 3.8 10.5 - - + -
52D ASN* 1.3 73.1 - - - +
54D GLY* 1.3 59.7 + - - +
55D LEU* 3.9 30.6 + - + +
77D VAL* 5.5 1.3 - - + -
169D PHE* 4.2 18.6 - - + -
172D ALA* 5.5 2.5 - - + -
173D ILE* 4.1 25.4 - - + -
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Residues in contact with GLY 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1529C MET* 3.7 19.5 - - - -
4D ILE 2.9 10.5 + - - +
5D LYS* 3.9 1.6 - - - -
6D CYS* 2.9 31.2 + - - +
40D TYR 3.7 2.0 - - - -
41D SER* 4.5 3.1 - - - -
52D ASN* 3.7 6.1 + - - -
53D LEU* 1.3 73.4 - - - +
55D LEU* 1.3 61.1 + - - -
56D TRP* 4.0 4.8 + - - -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1529C MET* 3.5 1.1 - - - -
6D CYS* 3.4 36.3 - - + +
8D VAL* 4.7 3.1 - - + -
20D LEU* 4.1 27.2 - - + +
23D TYR* 4.3 1.3 - - + -
24D THR* 3.8 28.5 - - + -
39D ASN* 3.1 24.3 - - - +
40D TYR* 2.7 19.9 + - + +
53D LEU* 4.1 24.0 - - + +
54D GLY* 1.3 73.2 - - - +
56D TRP* 1.3 62.9 + - - +
57D ASP 3.7 0.3 + - - -
169D PHE* 4.0 29.8 - - + -
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Residues in contact with TRP 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1525C ASN* 3.7 13.1 + - - +
1528C SER* 3.6 23.1 - - - -
1529C MET* 3.4 46.9 - - + +
1532C ASN* 4.6 7.2 - - + -
1595C LEU* 5.4 1.3 - - + -
1598C PHE* 3.7 29.6 - + - -
5D LYS* 3.4 49.5 - - + +
6D CYS 2.9 16.2 + - - +
7D VAL* 4.0 13.3 - - + +
8D VAL* 2.8 34.0 + - - +
20D LEU* 4.7 0.2 - - - -
39D ASN* 3.6 10.5 - - - -
54D GLY* 4.0 6.3 + - - -
55D LEU* 1.3 72.1 - - - +
57D ASP* 1.3 60.6 + - - +
58D THR* 3.6 3.3 + - + -
71D SER* 4.0 24.2 - - - -
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Residues in contact with ASP 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539C VAL* 3.2 35.3 - - - +
8D VAL* 4.3 2.2 - - - +
16D LYS* 3.4 28.6 - - - +
17D ASN* 3.7 20.7 - - - +
20D LEU* 3.4 26.0 - - + +
38D ASP* 4.4 7.7 - - + +
39D ASN* 3.0 27.9 + - - +
40D TYR* 4.7 1.9 - - + -
55D LEU 3.7 1.2 + - - -
56D TRP* 1.3 71.4 - - - +
58D THR* 1.3 63.5 + - - +
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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