Contacts of the helix formed by residues 17 - 30 (chain B) in PDB entry 2Q7V
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 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLY 3.5 3.6 - - - -
16B GLY* 1.3 77.0 - - - +
18B PRO* 1.4 70.9 - - - +
19B ALA 3.3 2.9 - - - -
20B GLY 3.2 1.9 + - - +
21B LEU* 2.9 31.7 + - - +
43B GLY 3.8 0.4 - - - -
44B GLY 3.8 9.9 - - - -
448B FAD 3.4 26.0 + - - -
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Residues in contact with PRO 18 (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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17B GLY* 1.4 81.8 - - - +
19B ALA* 1.3 60.0 + - - +
21B LEU* 4.2 1.7 - - + +
22B THR* 2.8 31.4 + - - -
43B GLY* 3.4 14.4 - - - +
46B ILE* 4.0 10.8 - - + -
71B MET* 4.0 21.9 - - - +
293B LEU* 3.4 34.5 - - + -
296B SER* 4.5 3.8 - - - -
297B VAL* 3.9 11.6 - - + +
448B FAD 3.4 30.1 - - - +
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Residues in contact with ALA 19 (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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18B PRO* 1.3 74.7 - - - +
20B GLY* 1.3 56.7 + - - +
22B THR* 3.7 0.4 - - - -
23B ALA* 3.0 28.2 + - - +
118B ALA* 4.1 4.5 - - + -
282B ALA* 3.7 24.9 - - + +
283B GLY* 3.8 3.1 - - - -
296B SER* 3.5 27.2 - - - +
300B GLY* 3.6 7.9 - - - -
448B FAD 2.9 32.7 + - - +
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Residues in contact with GLY 20 (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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13B ILE* 3.5 19.8 - - - +
15B GLY 3.4 24.0 + - - -
16B GLY* 4.8 0.2 - - - -
17B GLY 3.2 5.4 + - - +
19B ALA* 1.3 75.9 - - - +
21B LEU* 1.3 61.4 + - - +
23B ALA* 3.4 4.1 + - - +
24B ALA* 3.0 27.5 + - - +
36B ILE* 4.6 1.7 - - - +
118B ALA* 3.8 8.6 - - - +
448B FAD 4.1 0.4 + - - -
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Residues in contact with LEU 21 (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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16B GLY* 3.4 25.6 - - - +
17B GLY 2.9 19.4 + - - +
18B PRO* 4.2 3.6 - - + +
20B GLY* 1.3 78.0 - - - +
22B THR* 1.3 63.3 + - - +
24B ALA* 3.2 5.5 + - - +
25B ILE* 3.0 28.4 + - - +
36B ILE* 3.9 23.1 - - + -
42B PRO* 4.7 8.1 - - + -
43B GLY* 4.1 13.2 - - - +
68B ALA 4.2 3.4 - - - +
71B MET* 3.8 23.8 - - + +
72B HIS* 3.8 32.5 - - + +
75B ALA* 3.6 11.2 - - + +
82B VAL* 5.3 1.1 - - + -
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Residues in contact with THR 22 (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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56A PRO* 3.4 26.3 - - + +
18B PRO 2.8 22.6 + - - -
19B ALA 3.7 3.6 - - - -
21B LEU* 1.3 74.9 - - - +
23B ALA* 1.3 65.5 + - - +
25B ILE* 3.2 20.7 + - + +
26B TYR* 3.2 18.4 + - + -
71B MET* 4.9 1.4 - - - -
297B VAL* 3.3 30.7 - - - +
300B GLY* 4.7 0.2 - - - -
301B THR* 3.3 29.2 - - - +
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Residues in contact with ALA 23 (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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13B ILE* 3.9 7.6 - - + -
19B ALA 3.0 17.7 + - - +
20B GLY* 3.6 9.2 - - - +
22B THR* 1.3 74.4 - - - +
24B ALA* 1.3 57.7 + - - +
26B TYR 3.3 2.1 + - - -
27B THR* 2.9 30.7 + - - -
116B ILE* 3.9 29.8 - - + -
300B GLY* 3.6 23.9 + - - +
304B ALA* 3.4 5.5 - - - +
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Residues in contact with ALA 24 (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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13B ILE* 3.5 14.1 - - + +
20B GLY 3.0 16.8 + - - +
21B LEU 3.5 5.2 - - - +
22B THR 3.1 0.2 - - - -
23B ALA* 1.3 74.1 - - - +
25B ILE* 1.3 59.1 + - - +
27B THR* 3.6 4.7 - - - +
28B GLY* 2.9 28.9 + - - -
36B ILE* 3.5 27.8 - - + -
75B ALA* 4.1 5.6 - - + +
78B PHE* 5.0 0.2 - - - +
80B ALA* 3.7 18.9 - - + +
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Residues in contact with ILE 25 (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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54A ASN* 3.9 34.5 - - + +
56A PRO* 4.0 18.4 - - + -
21B LEU 3.0 17.9 + - - +
22B THR* 3.2 13.4 + - - +
24B ALA* 1.3 73.9 - - - +
26B TYR* 1.3 59.7 + - + +
29B ARG* 3.0 32.0 + - - +
71B MET* 4.5 5.8 - - + +
74B GLN* 3.5 32.5 - - + +
75B ALA* 3.8 22.2 - - - +
78B PHE* 3.9 23.2 - - + +
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Residues in contact with TYR 26 (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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54A ASN* 3.2 42.8 + - + -
144A THR* 3.7 15.7 - - + -
292A GLN* 2.6 40.1 + - + +
294A ALA* 4.7 4.4 - - + +
348A FAD 3.7 3.5 + - - -
22B THR* 3.2 18.7 + - + -
23B ALA 3.7 0.4 - - - +
25B ILE* 1.3 79.8 - - + +
27B THR* 1.3 59.9 - - - +
29B ARG* 3.3 5.4 + - - +
30B ALA* 2.9 31.4 + - - +
301B THR* 3.5 35.4 + - + +
304B ALA* 3.4 24.7 - - + -
305B MET* 3.9 16.6 - - + -
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Residues in contact with THR 27 (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 VAL* 3.5 24.2 - - + +
13B ILE* 4.1 3.1 - - + -
23B ALA 2.9 17.6 + - - +
24B ALA* 3.6 3.8 - - - +
26B TYR* 1.3 76.1 - - - +
28B GLY* 1.3 63.4 + - - +
30B ALA* 3.2 8.3 + - - +
31B GLN 3.4 0.2 + - - -
32B LEU* 3.1 37.9 + - - +
34B THR* 2.5 49.4 - - + +
116B ILE* 4.4 2.8 - - - +
304B ALA* 4.0 17.5 + - - +
307B THR* 4.5 1.4 - - - +
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Residues in contact with GLY 28 (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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148A PHE* 5.1 0.3 - - - -
24B ALA 2.9 17.2 + - - -
25B ILE 4.1 0.2 - - - -
27B THR* 1.3 76.4 - - - +
29B ARG* 1.3 60.1 + - - +
31B GLN* 2.9 25.6 + - - -
32B LEU 3.9 10.5 - - - -
34B THR* 4.2 2.2 - - - -
78B PHE 3.2 27.6 - - - +
79B GLY* 5.2 0.4 - - - -
80B ALA 4.8 4.9 - - - -
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Residues in contact with ARG 29 (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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53A GLU* 3.0 42.3 + - - +
54A ASN* 4.0 27.1 - - - +
144A THR 3.0 19.0 + - - -
145A CYS 3.0 29.2 + - - -
146A ASP* 4.8 2.0 - - - +
148A PHE* 3.3 43.7 - - + +
149A PHE* 4.9 4.0 - - - +
174A PHE* 3.6 8.0 - - - -
25B ILE 3.0 19.5 + - - +
26B TYR* 3.8 6.5 - - - +
28B GLY* 1.3 76.7 - - - +
30B ALA* 1.3 57.2 + - - +
31B GLN* 3.2 14.7 + - - -
78B PHE* 3.7 33.1 - - + +
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Residues in contact with ALA 30 (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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170A PHE* 4.7 11.0 - - + -
173A LYS* 2.5 32.0 + - - +
174A PHE* 4.5 7.6 - - - -
26B TYR 2.9 17.6 + - - +
27B THR* 3.5 6.7 - - - +
28B GLY 3.1 0.6 - - - -
29B ARG* 1.3 76.0 - - - +
31B GLN* 1.3 60.8 + - - +
32B LEU* 3.3 5.3 + - + +
308B GLU* 4.3 30.5 - - + +
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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