Contacts of the helix formed by residues 13 - 28 (chain A) in PDB entry 2I3B
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 GLY 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 1.3 79.1 - - - +
14A LYS* 1.3 62.2 + - - +
15A THR* 3.1 6.2 + - - -
16A THR* 2.9 32.0 + - - -
17A LEU* 3.5 14.2 - - - +
173A ARG* 4.0 10.1 - - - +
174A ASN* 5.2 1.8 - - - +
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Residues in contact with LYS 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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6A LEU* 3.7 24.5 - - + +
7A THR 4.9 4.1 + - - +
8A GLY* 4.6 5.5 + - - +
9A PRO 2.7 33.6 + - - -
10A PRO* 3.8 9.3 - - - +
11A GLY 4.8 0.2 - - - +
12A VAL* 4.7 12.1 - - - +
13A GLY* 1.3 75.0 - - - +
15A THR* 1.3 68.2 + - - +
17A LEU* 3.0 18.1 + - - +
18A ILE* 3.0 25.8 + - - +
112A ASP* 5.2 0.9 - - - +
142A THR* 3.6 27.6 - - + +
168A VAL* 4.2 33.2 - - + +
173A ARG* 4.2 9.2 - - - +
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Residues in contact with THR 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.5 14.1 - - + +
13A GLY* 3.9 13.9 + - - -
14A LYS* 1.3 81.1 - - - +
16A THR* 1.3 60.3 + - - +
18A ILE* 3.5 7.1 + - - +
19A HIS* 3.0 46.6 + - + +
37A THR 5.0 8.5 - - - +
38A GLU* 6.5 0.7 - - + -
112A ASP* 3.7 30.5 + - + +
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Residues in contact with THR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY* 2.9 13.0 + - - -
15A THR* 1.3 79.3 - - - +
17A LEU* 1.3 65.2 + - + +
18A ILE 3.3 0.2 - - - -
19A HIS* 3.5 19.5 - - + -
20A LYS* 2.9 46.3 + - + +
174A ASN* 6.1 0.4 - - - -
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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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6A LEU* 6.1 0.7 - - + -
13A GLY 3.5 23.7 + - - +
14A LYS* 3.0 17.1 + - + +
16A THR* 1.3 78.8 - - + +
18A ILE* 1.3 64.1 + - - +
20A LYS* 3.5 16.8 + - + +
21A ALA* 3.0 18.4 + - - +
168A VAL* 5.4 1.6 - - + -
173A ARG* 3.2 31.0 - - + +
174A ASN* 3.4 35.0 - - + +
176A LEU* 4.9 3.6 - - + -
177A LEU* 3.5 45.4 - - + +
180A ILE* 5.4 4.9 - - + -
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.5 39.7 - - + -
14A LYS 3.0 16.9 + - - +
15A THR* 3.5 9.2 - - - +
17A LEU* 1.3 73.8 - - - +
19A HIS* 1.3 68.8 + - + +
21A ALA* 2.9 16.4 + - + +
22A SER* 2.9 18.3 + - - +
36A TYR* 6.5 0.2 - - + -
110A VAL* 4.1 21.1 - - + -
112A ASP* 5.2 9.0 - - + +
140A LEU* 3.9 36.1 - - + +
141A GLY* 4.8 5.4 - - - +
142A THR* 4.2 9.6 - - - +
180A ILE* 4.5 9.9 - - + -
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Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 3.0 38.8 + - + +
16A THR* 3.2 26.6 + - + +
18A ILE* 1.3 76.9 - - + +
20A LYS* 1.3 57.9 + - + +
22A SER* 2.9 30.8 + - - -
23A GLU* 3.3 12.6 - - - +
36A TYR* 3.3 57.6 - + + +
37A THR 5.4 0.4 + - - -
38A GLU* 5.1 6.9 - - - +
54A LEU* 6.0 0.6 - - - +
112A ASP* 6.3 0.9 - - + -
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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
----------------------------------------------------------
16A THR* 2.9 33.9 + - + +
17A LEU* 3.7 22.9 - - + +
19A HIS* 1.3 74.6 - - + +
21A ALA* 1.3 57.8 + - - +
23A GLU* 3.0 40.4 + - - +
24A VAL* 3.4 10.7 + - - +
174A ASN* 5.4 4.6 + - - -
177A LEU* 3.7 22.8 - - + +
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Residues in contact with ALA 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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17A LEU 3.0 13.6 + - - +
18A ILE* 2.9 16.0 + - + +
20A LYS* 1.3 74.6 - - - +
22A SER* 1.3 55.1 + - - +
23A GLU 3.3 2.9 + - - -
24A VAL* 3.5 19.2 + - - +
25A LEU* 3.6 22.4 - - + +
140A LEU* 4.9 13.7 - - + -
177A LEU* 3.4 17.6 - - + +
180A ILE* 5.1 9.9 - - + -
181A VAL* 4.2 9.6 - - + -
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 2.9 15.6 + - - +
19A HIS* 2.9 19.8 + - - -
21A ALA* 1.3 74.1 - - - +
23A GLU* 1.3 58.7 + - - +
26A LYS* 3.1 30.8 + - - +
32A VAL* 4.1 13.2 - - - +
54A LEU* 4.0 22.4 - - - +
110A VAL* 3.8 22.3 - - - +
140A LEU* 5.1 0.7 - - - +
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Residues in contact with GLU 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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19A HIS* 3.3 16.2 - - - +
20A LYS* 3.0 22.8 + - - +
22A SER* 1.3 78.1 - - - +
24A VAL* 1.3 60.2 + - + +
26A LYS* 3.4 12.4 - - - +
27A SER* 2.9 26.7 + - - -
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Residues in contact with VAL 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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20A LYS 3.7 7.9 - - - +
21A ALA* 3.5 17.5 + - - +
23A GLU* 1.3 76.6 - - + +
25A LEU* 1.3 67.9 + - + +
26A LYS 3.0 0.4 - - - -
27A SER* 3.1 10.7 + - - +
28A SER* 2.9 28.5 + - - -
177A LEU* 4.8 6.1 - - + -
181A VAL* 3.7 37.7 - - + -
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Residues in contact with LEU 25 (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 ALA* 3.6 20.4 - - + +
24A VAL* 1.3 85.2 - - + +
26A LYS* 1.3 56.8 + - - +
28A SER* 3.0 10.0 + - - -
29A GLY 2.9 9.5 + - - -
30A VAL* 2.8 52.9 + - + +
32A VAL* 4.3 12.8 - - + -
108A VAL* 3.9 31.0 - - + -
140A LEU* 5.8 4.7 - - + -
181A VAL* 4.9 13.5 - - + -
184A VAL* 3.8 29.2 - - + -
185A GLN* 5.5 5.6 - - + +
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Residues in contact with LYS 26 (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 SER 3.1 25.6 + - - +
23A GLU* 3.4 11.3 + - - +
24A VAL 3.0 0.6 - - - -
25A LEU* 1.3 77.8 - - - +
27A SER* 1.3 55.2 + - - +
29A GLY* 3.0 18.4 + - - +
30A VAL 3.8 8.5 - - - +
31A PRO* 5.0 4.3 - - + -
32A VAL* 3.3 34.1 - - + +
54A LEU* 4.0 31.8 + - - +
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Residues in contact with SER 27 (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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23A GLU 2.9 18.0 + - - -
24A VAL* 3.1 11.6 + - - -
26A LYS* 1.3 74.7 - - - +
28A SER* 1.3 56.5 + - - +
29A GLY 3.4 1.0 + - - -
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL 2.9 15.1 + - - -
25A LEU* 3.0 13.9 + - - -
27A SER* 1.3 76.8 - - - +
29A GLY* 1.3 57.2 + - - +
30A VAL* 3.3 11.8 + - - +
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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