Contacts of the strand formed by residues 11 - 17 (chain A) in PDB entry 2DHI
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 SER 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.7 11.8 + - - -
10A LYS* 1.3 80.3 + - - +
12A GLY* 1.3 58.0 + - - +
28A TRP* 3.5 17.4 - - - -
29A PHE 3.7 1.6 - - - -
30A ASP* 2.7 30.3 - - - -
105A TRP* 4.6 1.1 - - - -
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Residues in contact with GLY 12 (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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10A LYS* 5.9 2.0 - - - -
11A SER* 1.3 75.8 - - - +
13A TRP* 1.3 60.3 - - - -
14A LEU* 4.6 4.0 - - - -
28A TRP* 2.9 27.6 - - - -
29A PHE* 3.1 23.3 + - - +
101A ASP* 6.1 0.4 - - - -
105A TRP* 4.0 11.5 - - - -
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Residues in contact with TRP 13 (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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12A GLY* 1.3 70.1 - - - -
14A LEU* 1.3 79.2 + - - +
26A LYS* 3.5 54.0 + - + +
27A ASN* 2.9 33.9 - - - -
28A TRP* 3.1 34.1 - + + -
41A ASP 4.4 1.1 - - - -
42A ASP* 3.6 23.6 - - + -
43A GLN* 3.1 43.9 - - + +
97A GLU* 5.2 3.3 + - - +
101A ASP* 4.1 3.5 - - - +
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Residues in contact with LEU 14 (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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12A GLY 4.0 2.8 + - - +
13A TRP* 1.3 91.8 - - - +
15A LEU* 1.3 62.4 + - - +
26A LYS* 4.5 4.2 - - - +
27A ASN* 2.7 42.4 + - - +
29A PHE* 3.6 30.4 - - + -
82A LEU* 5.5 3.4 - - + -
94A LEU* 5.1 10.8 - - + -
95A CYS 3.7 7.6 - - - +
96A ALA* 4.0 16.4 - - + +
101A ASP* 3.1 25.1 - - - +
105A TRP* 3.0 45.1 - - + +
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Residues in contact with LEU 15 (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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14A LEU* 1.3 74.7 - - - +
16A ARG* 1.3 60.4 + - - +
24A TRP* 3.7 23.6 - - + +
25A LYS 3.3 11.4 - - - +
26A LYS* 3.5 43.3 - - + +
73A PRO* 3.9 17.7 - - + -
76A LYS* 5.4 8.1 - - + -
94A LEU* 3.1 29.6 - - - +
95A CYS* 3.1 39.8 + - + +
96A ALA 5.3 2.7 - - - +
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Residues in contact with ARG 16 (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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15A LEU* 1.3 77.8 - - - +
17A GLN* 1.3 71.8 + - - +
18A SER* 3.2 19.2 + - - +
23A ARG 3.3 9.4 - - - +
24A TRP* 4.3 1.8 - - - -
25A LYS* 3.0 24.2 + - + +
27A ASN* 3.2 21.3 - - - +
29A PHE* 4.1 11.0 - - + -
39A TYR* 3.7 39.2 + - - -
49A GLU* 4.6 6.6 + - - -
50A ASP* 5.6 2.0 + - - +
90A LYS* 4.9 6.3 - - - +
92A ILE* 3.3 40.7 - - + +
93A SER 3.3 3.1 - - - -
94A LEU* 3.6 13.0 - - + -
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Residues in contact with GLN 17 (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 ARG* 1.3 76.3 + - - +
18A SER* 1.3 69.4 + - - +
19A THR* 4.0 1.2 + - - -
22A LYS* 4.4 6.8 - - - +
23A ARG* 3.3 28.3 - - - +
24A TRP* 3.4 38.0 - - + +
70A ILE* 4.2 16.4 - - - +
71A GLN* 4.2 6.9 + - - +
92A ILE* 5.8 0.7 - - - +
93A SER* 3.0 33.9 + - - +
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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