Contacts of the helix formed by residues 2 - 17 (chain B) in PDB entry 1C3Q
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 ASP 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-6B HIS* 4.3 2.5 - - - -
0B SER* 3.8 7.9 - - - +
1B MET* 1.3 79.5 - - - +
3B ALA* 1.3 65.9 + - - +
4B GLN* 3.6 23.9 - - - +
5B SER* 3.0 24.6 + - - -
6B ALA* 3.0 17.5 + - - +
266B ILE* 3.8 12.2 - - - +
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Residues in contact with ALA 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASP* 1.3 74.5 - - - +
4B GLN* 1.3 63.6 + - - +
6B ALA* 3.1 9.5 + - - +
7B ALA* 2.9 25.8 + - - +
260B VAL* 3.6 11.5 - - - +
261B GLN* 3.9 14.5 - - - +
264B ALA* 3.5 37.9 - - + +
266B ILE* 3.7 6.9 - - + +
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Residues in contact with GLN 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASP* 3.1 21.2 - - - +
3B ALA* 1.3 80.8 - - - +
5B SER* 1.3 64.4 + - - +
7B ALA* 3.4 4.7 + - - +
8B LYS* 3.3 31.5 + - + +
261B GLN* 4.1 20.9 - - + +
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Residues in contact with SER 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-7B HIS* 3.7 15.7 + - - +
-6B HIS* 2.9 33.8 - - - -
1B MET* 3.9 12.8 - - - -
2B ASP* 3.0 15.0 + - - -
4B GLN* 1.3 78.5 + - - +
6B ALA* 1.3 66.3 + - - +
8B LYS* 3.0 21.2 + - - +
9B CYS* 3.1 16.6 + - - -
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Residues in contact with ALA 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.5 12.9 - - + +
2B ASP 3.0 11.3 + - - +
3B ALA* 3.1 14.8 + - - +
5B SER* 1.3 76.3 - - - +
7B ALA* 1.3 63.4 + - - +
9B CYS* 3.2 5.4 + - - +
10B LEU* 3.2 19.8 + - - +
220B ALA* 3.7 27.9 - - - +
223B SER* 4.7 2.9 - - - -
224B SER* 4.4 2.5 + - - -
260B VAL* 4.0 12.8 - - + -
266B ILE* 4.4 9.0 - - + -
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Residues in contact with ALA 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ALA 2.9 10.2 + - - +
4B GLN 3.6 2.9 - - - +
5B SER 3.2 0.2 - - - -
6B ALA* 1.3 76.5 - - - +
8B LYS* 1.3 63.4 + - - +
10B LEU* 3.3 7.7 + - - +
11B THR* 3.2 24.3 + - - -
257B GLU* 3.2 42.5 - - + +
260B VAL* 3.8 14.1 - - + +
261B GLN* 3.5 17.3 - - + +
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-7B HIS* 4.4 21.5 - - + +
4B GLN* 3.3 22.4 + - + +
5B SER* 3.0 14.7 + - - +
7B ALA* 1.3 79.1 - - - +
9B CYS* 1.3 62.3 + - - +
11B THR* 3.3 7.6 + - + +
12B ALA* 3.0 20.5 + - - +
15B ARG* 4.9 1.9 + - - -
257B GLU* 2.7 27.1 + - - +
261B GLN* 4.5 8.3 + - - -
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Residues in contact with CYS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-7B HIS* 3.9 26.9 - - - -
-6B HIS* 6.3 0.9 - - - -
1B MET* 4.7 7.0 - - - -
5B SER* 3.1 18.3 + - - -
6B ALA 3.2 7.6 + - - +
8B LYS* 1.3 74.2 - - - +
10B LEU* 1.3 66.2 + - - +
12B ALA* 3.1 9.5 + - - +
13B VAL* 3.0 26.9 + - - +
207B PHE* 3.8 20.6 - - + -
210B VAL* 4.2 2.7 - - + +
211B GLU* 4.2 21.8 - - + -
216B PHE* 5.0 0.7 - - - -
220B ALA* 3.8 11.9 - - + -
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ALA 3.2 12.2 + - - +
7B ALA* 3.5 9.4 - - - +
8B LYS 3.2 0.2 - - - -
9B CYS* 1.3 77.4 - - - +
11B THR* 1.3 61.7 + - - +
13B VAL* 3.3 3.7 + - + +
14B ARG* 3.2 58.6 + - + +
39B LEU* 3.8 24.0 - - + -
207B PHE* 3.7 16.1 - - + -
224B SER* 4.1 12.8 - - - +
255B VAL* 4.2 12.1 - - + -
256B THR 4.2 10.3 - - - +
257B GLU* 4.5 2.7 - - - +
260B VAL* 3.7 27.4 - - + -
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Residues in contact with THR 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ALA 3.2 10.8 + - - -
8B LYS* 3.5 11.2 - - - -
10B LEU* 1.3 79.6 - - - +
12B ALA* 1.3 57.8 + - - +
14B ARG* 3.4 9.3 + - + +
15B ARG* 2.9 49.3 + - + +
257B GLU* 3.4 28.1 + - - +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-7B HIS* 3.5 33.4 - - + +
8B LYS 3.0 11.6 + - - +
9B CYS* 3.1 10.3 + - - +
11B THR* 1.3 74.3 - - - +
13B VAL* 1.3 64.2 + - - +
15B ARG* 3.3 17.6 + - - +
16B HIS* 3.0 35.5 + - + +
210B VAL* 4.1 11.4 - - + -
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B CYS 3.0 19.4 + - - +
10B LEU* 3.3 8.5 + - + +
12B ALA* 1.3 76.3 - - - +
14B ARG* 1.3 54.6 + - + +
17B SER* 2.7 33.8 + - - -
18B PRO* 3.3 17.5 - - + +
39B LEU* 4.2 29.8 - - + +
40B GLY 4.0 0.6 - - - +
41B ALA* 4.4 8.7 - - + +
206B ALA* 3.9 16.4 - - + +
207B PHE* 3.9 25.6 - - + -
210B VAL* 3.8 18.4 - - + +
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 3.2 37.6 + - + +
11B THR* 3.9 9.2 - - + +
12B ALA 3.3 0.2 - - - -
13B VAL* 1.3 77.8 - - + +
15B ARG* 1.3 60.8 + - - +
17B SER* 3.9 8.7 + - - -
38B ALA 5.3 0.2 + - - -
39B LEU 3.1 25.6 + - - +
40B GLY* 4.3 11.7 - - - +
252B LEU 3.0 25.9 + - - -
253B SER 3.6 12.1 + - - -
255B VAL* 2.7 41.8 + - - +
256B THR* 4.4 5.1 - - - +
257B GLU 4.9 1.0 - - - +
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-7B HIS* 4.8 6.9 + - - -
8B LYS 4.9 1.8 + - - -
11B THR* 2.9 35.0 + - + +
12B ALA* 3.6 26.7 - - - +
14B ARG* 1.3 78.0 - - - +
16B HIS* 1.3 83.4 + - + +
17B SER* 5.2 0.9 - - - -
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Residues in contact with HIS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-11B MET* 2.9 63.6 + - + +
-7B HIS* 5.8 1.4 + - - -
12B ALA* 3.0 34.9 + - + +
15B ARG* 1.3 103.6 + - + +
17B SER* 1.3 72.3 + - - +
18B PRO* 3.2 4.6 - - + +
210B VAL* 4.1 13.9 - - + -
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 5.9 0.3 + - - -
13B VAL 2.7 18.1 + - - -
14B ARG 3.9 5.7 + - - -
15B ARG 3.6 0.8 - - - -
16B HIS* 1.3 75.3 - - - +
18B PRO* 1.3 70.8 - - - +
19B LEU* 3.6 1.0 + - - +
40B GLY 3.1 22.0 + - - -
41B ALA 3.7 1.6 + - - -
42B SER* 2.6 33.3 + - - -
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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