Contacts of the strand formed by residues 13 - 24 (chain A) in PDB entry 2CND
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 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY 3.2 16.6 - - - +
12A ARG* 1.3 86.3 - - - +
14A HIS* 1.3 63.2 + - - +
15A CYS* 4.0 7.9 - - - -
34A LEU* 4.7 6.1 - - + -
35A PRO* 3.6 28.5 - - + -
39A GLN* 5.7 7.0 - - - +
41A LEU* 4.5 17.5 - - + -
111A ASP* 3.5 4.5 - - - -
112A VAL* 3.0 46.0 + - + +
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Residues in contact with HIS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 5.9 0.7 - - - -
13A ILE* 1.3 75.7 - - - +
15A CYS* 1.3 60.5 + - - +
16A ARG 4.3 0.2 + - - -
35A PRO* 3.2 32.0 - - + +
109A TYR* 3.8 39.9 - + + +
110A ILE 3.1 25.1 - - - -
111A ASP* 3.2 22.9 + - - -
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Residues in contact with CYS 15 (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 ILE* 4.3 3.8 - - - -
14A HIS* 1.3 78.1 - - - +
16A ARG* 1.3 57.2 + - - +
32A PHE* 4.0 17.9 - - + -
33A SER 3.1 17.7 - - - +
34A LEU* 4.1 9.0 - - - -
76A PHE* 3.5 22.2 - - + -
109A TYR* 3.3 4.9 - - - -
110A ILE* 2.6 46.3 + - + +
112A VAL* 3.3 34.3 - - - -
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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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14A HIS 4.3 0.4 + - - -
15A CYS* 1.3 74.4 - - - +
17A LEU* 1.3 62.6 + - - +
18A VAL* 3.3 11.6 + - - +
32A PHE* 3.3 6.1 - - - -
33A SER* 2.9 42.9 + - - +
107A GLY* 2.7 53.1 + - - +
108A SER 3.2 4.7 - - - +
109A TYR* 3.0 44.8 + - + +
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Residues in contact with LEU 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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15A CYS 4.1 0.6 + - - -
16A ARG* 1.3 70.2 + - - +
18A VAL* 1.3 60.7 + - - +
19A ALA 3.4 24.5 - - - +
20A LYS* 4.3 7.0 - - - -
30A PHE* 3.8 20.2 - - + -
31A ARG 4.4 0.9 - - - +
32A PHE* 3.7 32.5 - - + -
101A LEU* 5.0 1.8 - - + +
104A LEU* 3.8 27.8 - - + +
105A PRO 3.7 21.3 - - - +
106A VAL* 3.6 16.5 - - + +
107A GLY* 3.1 23.6 + - - +
108A SER* 2.7 19.4 + - - +
110A ILE* 5.3 2.7 - - + -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.3 13.8 + - - +
17A LEU* 1.3 75.5 - - - +
19A ALA* 1.3 66.1 + - + +
31A ARG* 2.9 33.1 + - + +
33A SER* 3.6 30.7 - - - +
75A HIS* 4.7 8.7 - - + +
106A VAL* 4.2 11.6 - - - +
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Residues in contact with ALA 19 (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 LEU* 3.4 11.2 - - - +
18A VAL* 1.3 90.1 - - + +
20A LYS* 1.3 61.5 + - - +
29A LEU 4.4 0.7 - - - -
30A PHE* 3.3 3.8 - - - -
31A ARG* 2.9 35.9 + - + -
106A VAL* 4.3 7.9 - - - -
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Residues in contact with LYS 20 (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 LEU* 4.3 7.6 - - + -
19A ALA* 1.3 76.1 - - - +
21A LYS* 1.3 69.2 + - - +
22A GLU* 5.6 5.2 - - + -
28A ARG* 4.1 15.7 - - + -
29A LEU 3.3 4.7 - - - -
30A PHE* 3.2 33.2 - - + -
101A LEU 2.9 25.0 + - - -
102A ASP* 3.0 22.7 + - - +
104A LEU 3.0 23.4 + - - -
106A VAL* 4.1 15.1 - - + +
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Residues in contact with LYS 21 (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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20A LYS* 1.3 79.6 + - - +
22A GLU* 1.3 67.1 + - - +
23A LEU* 3.4 29.4 + - + -
28A ARG* 2.9 10.0 - - - -
29A LEU* 2.7 64.5 + - + +
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Residues in contact with GLU 22 (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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20A LYS* 5.6 5.2 - - + -
21A LYS* 1.3 79.3 - - - +
23A LEU* 1.3 63.2 + - - +
24A SER 3.2 3.8 - - - +
28A ARG* 2.8 48.4 + - + +
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Residues in contact with LEU 23 (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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21A LYS* 3.4 32.0 + - + +
22A GLU* 1.3 71.8 - - - +
24A SER* 1.3 64.1 - - - +
27A VAL* 2.8 26.4 + - + -
29A LEU* 4.3 21.3 - - + +
79A LEU* 3.5 31.9 - - + -
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Residues in contact with SER 24 (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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22A GLU* 3.2 4.3 - - - -
23A LEU* 1.3 82.1 - - - +
25A ARG* 1.3 58.4 + - - +
26A ASP* 2.7 19.2 + - - -
27A VAL* 2.9 35.3 + - - +
28A ARG* 2.9 18.3 + - - -
179A ASP 5.3 6.8 + - - -
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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