Contacts of the helix formed by residues 4 - 16 (chain B) in PDB entry 2ORY
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 THR 4 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B TYR* 1.3 78.3 - - - +
5B LYS* 1.3 63.6 + - - +
6B GLU* 3.3 19.9 - - + +
7B GLN* 2.8 41.9 + - - +
8B LEU* 3.0 21.9 + - - +
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Residues in contact with LYS 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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4B THR* 1.3 73.4 - - - +
6B GLU* 1.3 68.2 + - - +
8B LEU* 3.2 11.8 + - + +
9B MET* 2.8 40.8 + - + +
169B CYS* 3.7 26.4 - - - +
202B SER* 2.9 31.3 + - - -
204B ILE* 4.0 14.1 - - + +
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Residues in contact with GLU 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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4B THR* 3.3 21.8 - - + +
5B LYS* 1.3 93.3 + - - +
7B GLN* 1.3 55.5 + - + +
9B MET* 3.2 1.5 + - - -
10B LEU* 2.8 25.3 + - - +
204B ILE* 4.2 20.4 - - + +
206B PHE* 3.4 11.0 - - - -
229B THR* 4.5 15.2 + - - +
231B ILE* 3.9 25.1 - - + -
320B MET* 5.3 4.3 - - - -
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Residues in contact with GLN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.3 16.5 - - + -
4B THR* 2.8 45.6 + - - +
6B GLU* 1.3 76.7 - - + +
8B LEU* 1.3 63.9 + - - +
10B LEU* 3.2 8.4 + - - +
11B ALA 3.1 17.2 + - - -
320B MET* 3.2 31.7 + - + +
321B GLY* 4.5 4.4 + - - -
322B MET* 3.2 40.3 - - + +
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Residues in contact with LEU 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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3B TYR* 5.0 7.1 - - + +
4B THR 3.0 13.7 + - - +
5B LYS* 3.4 14.6 - - + +
7B GLN* 1.3 74.5 - - - +
9B MET* 1.3 70.9 + - - +
11B ALA* 3.1 15.9 + - - +
12B PHE* 3.1 24.6 + - + -
46B PRO* 3.5 29.8 - - + +
47B PHE* 4.0 20.0 - - + -
52B TRP* 3.7 31.4 - - + +
78B LYS* 6.1 1.3 - - - +
86B VAL* 6.0 0.7 - - + -
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Residues in contact with MET 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS* 2.8 30.3 + - + +
6B GLU 3.7 4.5 - - - +
8B LEU* 1.3 76.2 - - - +
10B LEU* 1.3 63.1 + - - +
12B PHE* 3.3 7.6 + - - +
13B SER* 2.9 27.5 + - - -
86B VAL* 3.2 44.2 - - + -
169B CYS* 3.0 35.2 - - + +
171B THR* 3.3 30.9 + - - +
204B ILE* 3.8 21.3 - - + -
206B PHE* 3.9 7.6 - - + -
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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 GLU 2.8 13.5 + - - +
7B GLN* 3.3 10.5 - - - +
8B LEU 3.1 0.2 - - - -
9B MET* 1.3 76.3 - - - +
11B ALA* 1.3 57.1 + - - +
13B SER* 3.2 1.5 + - - -
14B TYR* 2.8 60.5 + - + -
206B PHE* 3.6 25.5 - - + -
316B TYR* 3.8 4.0 - - + -
317B PRO* 3.8 19.1 - - + -
320B MET* 3.2 36.1 - - + -
322B MET* 4.0 13.5 - - + -
326B ILE* 3.8 20.9 - - + -
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLN 3.1 10.8 + - - +
8B LEU 3.1 9.0 + - - +
10B LEU* 1.3 77.9 - - - +
12B PHE* 1.3 56.5 + - - +
14B TYR 3.2 0.5 + - - -
15B MET* 2.8 31.2 + - - +
44B TRP* 3.5 12.6 - - + -
46B PRO* 4.0 22.4 - - + -
47B PHE* 3.4 23.6 - - + -
322B MET* 4.3 4.3 - - + -
326B ILE* 4.1 11.2 - - + +
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Residues in contact with PHE 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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8B LEU* 3.1 38.0 + - + -
9B MET* 3.7 11.0 - - - +
11B ALA* 1.3 75.5 - - - +
13B SER* 1.3 63.0 + - - +
15B MET* 3.3 8.5 + - + -
16B SER* 3.2 8.9 + - - -
41B LEU* 4.4 8.1 - - + -
47B PHE* 3.3 29.8 - + - -
52B TRP* 3.7 33.9 - + - -
74B TYR* 2.7 32.6 + - - +
76B ILE* 3.8 27.4 - - + -
86B VAL* 4.0 32.5 - - + -
88B ALA* 4.3 3.6 - - + -
171B THR* 4.2 11.2 - - + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B MET 2.9 11.6 + - - -
10B LEU* 3.5 5.2 - - - -
12B PHE* 1.3 76.6 - - - +
14B TYR* 1.3 62.2 + - - +
16B SER* 3.2 26.1 - - - -
17B TYR* 4.0 10.4 - - - -
88B ALA* 4.9 0.7 - - - -
89B ILE 5.3 0.3 - - - +
90B ARG* 5.3 0.2 - - - +
171B THR* 2.9 29.8 + - - +
172B GLY* 3.1 17.7 + - - -
173B HIS* 4.0 23.4 + - - +
206B PHE* 3.8 7.8 - - - -
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Residues in contact with TYR 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* 2.8 45.4 + - + +
11B ALA 3.2 3.1 + - - +
13B SER* 1.3 78.6 - - - +
15B MET* 1.3 60.4 + - - +
16B SER 3.0 4.9 - - - -
17B TYR* 3.1 25.1 + + - +
44B TRP* 4.7 0.2 - - + -
173B HIS* 3.4 39.3 + + + -
313B VAL* 2.6 38.5 + - + -
316B TYR* 3.7 4.7 - - - +
317B PRO* 3.6 12.1 - - + +
326B ILE* 3.7 26.2 - - + -
328B LEU* 3.7 26.5 - - + -
331B ILE* 3.6 13.4 - - + +
332B PHE* 4.4 11.4 - + - -
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Residues in contact with MET 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 2.8 16.7 + - - +
12B PHE* 3.3 17.4 + - + +
14B TYR* 1.3 73.8 - - - +
16B SER* 1.3 63.6 + - - +
17B TYR 3.1 1.1 + - - -
18B TYR* 3.4 34.9 + - + +
37B MET* 3.9 33.6 - - + +
40B ALA* 3.7 25.4 - - + -
41B LEU* 4.2 15.9 - - + -
44B TRP* 3.8 14.1 - - + -
47B PHE* 3.9 10.1 - - + -
54B VAL* 5.1 2.2 - - + -
74B TYR* 3.3 36.8 - - + +
76B ILE* 5.0 0.9 - - + -
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE 3.2 15.3 + - - -
13B SER* 3.2 15.7 + - - -
15B MET* 1.3 79.3 - - - +
17B TYR* 1.3 58.1 + - - +
18B TYR 3.4 4.5 + - - +
33B ILE* 5.2 0.2 - - - +
37B MET* 5.0 0.2 - - - +
72B MET* 3.4 24.1 - - - +
74B TYR* 3.4 14.8 + - - -
88B ALA* 3.9 7.6 - - - +
89B ILE 4.3 6.5 + - - -
90B ARG* 3.1 43.7 + - - -
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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