Contacts of the strand formed by residues 32 - 38 (chain A) in PDB entry 2D7M
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 VAL 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.4 19.1 - - + +
20A GLY* 3.1 30.5 - - - +
26A ILE* 3.8 15.0 - - + -
27A PRO* 6.0 3.4 - - + +
30A LEU* 3.1 10.8 + - + +
31A PRO* 1.3 73.9 - - - +
33A GLU* 1.3 58.8 + - - +
73A SER* 4.3 0.9 - - - -
74A TYR* 2.7 88.9 + - + +
76A PRO* 4.2 2.9 - - + -
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Residues in contact with GLU 33 (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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19A PRO* 3.1 25.2 - - + +
20A GLY 4.1 1.6 - - - -
31A PRO 5.4 1.8 - - - +
32A VAL* 1.3 79.2 - - - +
34A PHE* 1.3 61.8 + - - +
35A THR* 5.2 2.1 + - - -
71A THR* 3.6 22.5 - - - +
72A VAL 2.8 17.9 - - - +
73A SER* 3.4 20.7 - - - -
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Residues in contact with PHE 34 (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 SER 3.9 5.6 - - - +
18A GLY* 4.4 1.1 - - - -
19A PRO* 4.4 2.9 - - - -
20A GLY* 4.1 6.1 - - - +
21A LEU* 3.5 53.8 - - + +
33A GLU* 1.3 75.9 - - - +
35A THR* 1.3 66.1 + - - +
36A ILE* 3.8 24.2 - - + -
48A VAL* 3.9 16.4 - - + -
50A ILE* 5.3 0.9 - - + -
71A THR* 3.4 7.8 - - - +
72A VAL* 2.8 71.9 + - + -
74A TYR* 3.9 29.8 - + - -
84A ILE* 4.9 4.5 - - + -
86A ILE* 4.4 6.7 - - + -
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Residues in contact with THR 35 (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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16A ALA* 4.1 0.3 - - - -
17A SER* 2.9 32.8 + - - +
18A GLY* 5.7 0.4 - - - -
33A GLU* 5.2 2.3 + - - -
34A PHE* 1.3 82.5 + - - +
36A ILE* 1.3 63.1 + - - +
37A ASP* 3.2 31.8 + - - +
65A ASN* 5.3 0.7 - - - +
69A THR* 4.6 7.4 - - - +
70A TYR 3.2 17.0 - - - +
71A THR* 4.1 11.2 + - - +
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Residues in contact with ILE 36 (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 VAL* 3.0 35.4 - - + -
15A ARG 3.3 2.7 - - - +
16A ALA* 4.1 18.6 - - + -
21A LEU* 4.2 0.7 - - + -
34A PHE* 3.8 33.9 - - + -
35A THR* 1.3 69.3 - - - +
37A ASP* 1.3 57.9 + - - +
38A ALA* 3.2 11.4 + - + -
46A LEU* 4.5 24.7 - - + -
48A VAL* 5.5 0.4 - - + -
69A THR* 3.3 0.5 - - - -
70A TYR* 2.7 46.4 + - + +
72A VAL* 4.8 4.3 - - + -
86A ILE* 3.9 21.3 - - + -
93A ILE* 5.9 0.2 - - + -
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Residues in contact with ASP 37 (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 LYS 4.2 2.1 - - - +
15A ARG* 3.0 37.1 + - + +
17A SER* 3.4 15.4 + - - -
35A THR* 3.2 27.6 - - - +
36A ILE* 1.3 69.3 - - - +
38A ALA* 1.3 58.3 + - - +
39A ARG* 4.3 9.9 + - - -
68A GLY 3.7 1.3 - - - -
69A THR* 3.4 26.0 - - + +
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Residues in contact with ALA 38 (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 LYS 3.9 4.3 - - - +
14A VAL* 3.9 22.4 - - + -
36A ILE* 3.2 9.7 + - + +
37A ASP* 1.3 73.9 - - - +
39A ARG* 1.3 61.3 + - - +
41A ALA* 3.3 29.1 - - + +
68A GLY* 2.4 30.0 + - - +
69A THR* 3.9 0.2 - - - +
70A TYR* 4.1 15.9 + - + -
88A TYR* 5.2 1.1 - - + -
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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