Contacts of the helix formed by residues 22 - 34 (chain B) in PDB entry 5GJQ
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 LEU 22 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 4.0 15.0 - - - +
15B ILE 3.3 31.4 - - - +
16B PHE* 3.8 13.9 - - + -
21B ARG* 1.3 78.1 - - - +
23B TYR* 1.3 66.5 + - - +
24B GLN 3.3 1.8 - - - -
25B VAL* 3.2 32.0 + - + +
26B GLU* 3.4 13.5 + - - +
126B THR* 3.7 19.3 - - + +
78C MET* 3.3 34.0 - - + +
127C ARG* 3.7 21.1 - - - +
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY* 3.6 10.0 - - - -
5B SER 3.5 9.1 + - - -
6B SER* 5.0 1.1 - - - -
10B ASP 3.4 28.1 + - - +
11B ARG* 3.1 49.7 + - + -
13B ILE 5.7 0.4 + - - -
15B ILE 4.8 0.8 + - - -
17B SER* 3.6 26.2 - - - -
19B GLU* 3.4 19.9 + - - -
21B ARG* 3.5 30.7 + - + -
22B LEU* 1.3 73.1 - - - +
24B GLN* 1.3 63.6 + - - +
26B GLU* 3.2 17.5 + - - +
27B TYR* 3.0 54.2 + + + -
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP 4.9 0.6 + - - -
11B ARG 3.0 24.2 + - - +
12B HIS* 3.0 33.5 + - - +
13B ILE* 3.8 14.5 + - - +
14B THR* 3.9 23.0 - - + +
22B LEU* 3.3 0.6 - - + -
23B TYR* 1.3 77.9 - - - +
25B VAL* 1.3 58.8 + - + +
27B TYR* 3.3 8.3 + - - +
28B ALA* 2.9 25.8 + - - +
132B ARG* 4.8 2.9 - - - +
133B PRO* 4.8 4.6 - - + +
12X SER 4.3 3.5 - - - +
13X THR* 3.7 4.3 - - - +
14X PHE* 2.9 59.7 + - - +
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 5.4 2.5 - - + -
22B LEU* 3.4 35.4 - - + +
23B TYR 3.1 0.4 - - - -
24B GLN* 1.3 77.4 - - + +
26B GLU* 1.3 68.0 + - + +
28B ALA* 3.0 17.5 + - - +
29B PHE* 3.0 21.2 + - + -
126B THR* 3.8 22.9 - - + +
133B PRO* 4.3 10.5 - - + -
156B PRO* 4.2 2.2 - - - +
157B ALA* 3.6 36.8 - - + +
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 2.5 59.2 + - - +
22B LEU 3.6 13.7 + - - +
23B TYR* 3.2 16.8 + - - +
25B VAL* 1.3 79.2 - - + +
27B TYR* 1.3 70.1 + - + +
29B PHE* 3.2 16.4 + - + +
30B LYS* 3.1 24.9 + - - +
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Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 3.3 52.6 + - + +
23B TYR* 3.0 39.1 + + + +
24B GLN* 3.4 13.9 - - - +
25B VAL 3.1 0.4 - - - -
26B GLU* 1.3 83.4 - - + +
28B ALA* 1.3 59.5 + - - +
30B LYS* 3.2 14.5 + - + +
31B ALA* 3.0 21.1 + - - +
7X TYR* 4.5 0.7 - + - -
14X PHE* 3.6 22.2 - - + -
15X SER 3.6 12.1 - - - +
16X PRO* 3.7 46.5 - - + +
18X GLY* 3.2 14.0 - - - -
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Residues in contact with ALA 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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24B GLN 2.9 9.8 + - - +
25B VAL 3.0 9.4 + - - +
27B TYR* 1.3 76.4 - - - +
29B PHE* 1.3 60.9 + - - +
31B ALA* 2.9 19.3 + - - +
32B ILE* 3.1 16.1 + - - +
133B PRO* 4.0 18.8 - - + -
134B LEU 4.3 3.8 - - - +
135B GLY* 4.0 2.3 - - - -
156B PRO* 4.0 11.7 - - + -
14X PHE* 3.4 30.5 - - + -
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Residues in contact with PHE 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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25B VAL* 3.0 33.5 + - + -
26B GLU* 3.2 15.5 + - + +
28B ALA* 1.3 75.1 - - - +
30B LYS* 1.3 64.1 + - + +
32B ILE* 3.2 31.1 + - + +
33B ASN* 4.1 7.8 + - - -
155B ASP* 3.5 44.4 - - + -
156B PRO* 3.7 11.9 - - + +
157B ALA* 3.8 26.0 - - + -
159B TYR* 5.5 1.3 - + - -
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Residues in contact with LYS 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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26B GLU 3.1 13.4 + - - +
27B TYR* 3.5 20.2 - - + +
28B ALA 3.1 0.2 - - - -
29B PHE* 1.3 75.3 - - + +
31B ALA* 1.3 64.5 - - - +
32B ILE 3.1 0.4 - - - -
33B ASN* 3.2 21.2 + - - +
34B GLN* 3.8 10.7 + - - +
16X PRO* 2.9 28.6 + - - +
17X ASP* 4.0 17.0 - - - +
18X GLY* 4.0 2.7 - - - -
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR 3.0 6.7 + - - +
28B ALA* 2.9 12.9 + - - +
30B LYS* 1.3 78.8 - - - +
32B ILE* 1.3 61.6 + - - +
33B ASN 3.3 0.2 - - - -
34B GLN* 3.4 16.9 + - - +
83B MET* 3.8 22.0 + - - +
135B GLY* 4.2 3.6 - - - -
14X PHE* 3.5 28.7 - - + -
18X GLY* 3.3 25.7 - - - +
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 3.1 11.6 + - - +
29B PHE* 3.3 22.7 - - + +
30B LYS 3.1 0.6 - - - -
31B ALA* 1.3 78.6 - - - +
33B ASN* 1.3 69.6 + - - +
34B GLN 3.3 1.2 + - - -
35B GLY* 3.7 4.0 + - - -
36B GLY 4.9 0.2 + - - -
37B LEU 5.8 0.9 + - - +
81B THR* 3.3 34.8 - - + +
82B GLY* 3.2 21.8 + - - -
135B GLY 4.0 14.1 - - - -
136B CYS 3.8 8.5 - - - +
137B CYS* 3.7 25.1 - - + -
156B PRO* 3.9 17.9 - - + -
168B ALA* 5.7 0.4 - - + -
169B GLY* 4.7 4.2 - - - +
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Residues in contact with ASN 33 (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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29B PHE 4.4 11.0 + - - -
30B LYS* 3.2 12.9 + - - +
32B ILE* 1.3 75.3 - - - +
34B GLN* 1.3 54.5 + - - +
35B GLY 3.1 3.4 - - - -
36B GLY* 2.8 28.6 + - - +
37B LEU 5.8 0.7 - - - +
169B GLY* 3.0 38.2 + - - +
170B VAL* 4.1 15.5 + - + +
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Residues in contact with GLN 34 (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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30B LYS 4.0 6.7 + - - +
31B ALA 3.5 13.2 - - - +
32B ILE 3.2 1.0 - - - -
33B ASN* 1.3 77.0 - - - +
35B GLY* 1.3 60.9 + - - +
36B GLY* 3.2 0.7 + - - -
83B MET* 5.5 4.7 - - + -
17X ASP* 2.7 29.5 + - - +
18X GLY 3.3 20.6 - - - +
19X ARG* 3.6 22.9 + - + +
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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