Contacts of the helix formed by residues 18 - 30 (chain j) 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 18 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9j THR 5.4 4.9 - - - +
11j ILE 4.0 19.1 - - - +
12j PHE* 3.7 34.8 - - + -
17j ARG* 1.3 75.5 - - - +
19j TYR* 1.3 65.4 + - - +
20j GLN* 3.2 2.7 - - + +
21j VAL* 3.2 36.9 + - + +
22j GLU* 3.3 15.1 + - - +
122j THR* 4.1 7.6 - - + +
153j SER* 6.3 1.3 - - - -
76k LEU* 4.6 11.4 - - + -
125k ARG* 3.0 39.3 - - - +
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Residues in contact with TYR 19 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335I GLU* 5.0 5.0 + - - +
11j ILE 5.0 2.8 + - - -
13j SER* 3.6 22.1 - - - -
14j PRO* 5.6 1.5 - - + +
15j GLU* 5.4 0.3 - - - +
17j ARG* 3.0 50.9 + - + -
18j LEU* 1.3 73.4 - - - +
20j GLN* 1.3 65.5 + - + +
22j GLU* 3.2 15.7 + - - +
23j TYR* 2.9 61.7 + + + -
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Residues in contact with GLN 20 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11i THR* 4.1 12.3 - - - +
12i PHE* 2.8 61.6 + - - +
7j SER* 5.4 2.6 + - - -
8j ARG 5.6 0.6 + - - -
9j THR* 4.0 43.7 + - - +
18j LEU* 3.2 2.3 - - + -
19j TYR* 1.3 79.4 - - + +
21j VAL* 1.3 59.9 + - + +
23j TYR* 3.8 9.2 - - - +
24j ALA* 3.0 28.8 + - - +
128j ARG* 4.5 1.6 - - - +
129j PRO* 3.8 20.7 - - + +
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Residues in contact with VAL 21 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18j LEU* 3.2 30.7 + - + +
19j TYR 3.1 0.4 - - - -
20j GLN* 1.3 79.8 - - + +
22j GLU* 1.3 58.6 + - + +
24j ALA* 3.2 7.3 + - - +
25j MET* 3.0 32.1 + - + +
122j THR* 3.9 27.6 - - + -
129j PRO* 4.6 10.3 - - + -
152j PRO* 4.2 7.4 - - + +
153j SER* 3.9 33.7 - - - +
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Residues in contact with GLU 22 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17j ARG* 3.8 40.5 + - + +
18j LEU 3.5 13.2 - - - +
19j TYR* 3.2 22.2 + - - +
21j VAL* 1.3 77.7 - - + +
23j TYR* 1.3 65.6 + - + +
25j MET* 3.1 11.3 + - - +
26j GLU* 2.9 30.0 + - - +
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Residues in contact with TYR 23 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12i PHE* 3.7 23.6 - - + -
13i SER 3.1 26.5 - - - +
14i PRO* 3.3 50.9 - - + +
16i GLY* 3.3 8.8 - - - -
19j TYR* 2.9 58.7 + + + +
20j GLN* 3.8 9.0 - - - +
22j GLU* 1.3 79.3 - - + +
24j ALA* 1.3 66.5 + - - +
26j GLU* 3.0 15.2 + - + +
27j ALA 3.0 10.0 + - - -
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Residues in contact with ALA 24 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12i PHE* 3.7 31.6 - - + -
20j GLN 3.0 19.9 + - - +
21j VAL* 3.4 7.9 - - - +
23j TYR* 1.3 78.6 - - - +
25j MET* 1.3 62.6 + - - +
27j ALA* 3.1 4.7 + - - +
28j ILE* 3.0 26.6 + - - +
129j PRO* 4.9 2.5 - - + -
131j GLY* 4.1 11.4 - - - +
152j PRO* 4.2 13.0 - - + -
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Residues in contact with MET 25 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21j VAL* 3.0 24.5 + - + +
22j GLU* 3.3 12.1 - - - +
24j ALA* 1.3 75.7 - - - +
26j GLU* 1.3 59.1 + - - +
28j ILE* 3.2 17.7 + - + +
29j GLY* 3.0 23.2 + - - -
133j SER* 4.8 0.7 - - - +
151j ASP* 3.5 24.9 - - - +
152j PRO* 3.6 30.3 - - + -
164j ILE* 5.4 4.5 - - + -
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Residues in contact with GLU 26 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14i PRO 4.1 13.0 - - - +
15i SER* 3.8 16.6 - - - +
22j GLU 2.9 15.2 + - - +
23j TYR* 3.0 13.9 + - + +
25j MET* 1.3 74.8 - - + +
27j ALA* 1.3 63.9 + - - +
29j GLY* 3.2 12.0 + - - +
30j HIS* 3.5 38.2 + - - -
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Residues in contact with ALA 27 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12i PHE* 4.3 0.7 - - + -
15i SER 4.6 1.3 - - - -
16i GLY* 3.1 33.5 - - - +
23j TYR 3.0 6.1 + - - +
24j ALA* 3.3 12.8 - - - +
26j GLU* 1.3 73.7 - - - +
28j ILE* 1.3 66.8 + - - +
30j HIS* 3.1 17.5 + - - +
31j ALA* 3.8 7.8 + - - +
78j GLY* 4.8 3.9 - - - -
79j ILE* 4.1 21.8 - - + -
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Residues in contact with ILE 28 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24j ALA 3.0 14.3 + - - +
25j MET* 3.4 19.1 - - + +
27j ALA* 1.3 75.6 - - - +
29j GLY* 1.3 63.6 + - - +
31j ALA* 3.1 17.8 + - - +
77j ALA* 3.8 19.7 - - + +
78j GLY* 4.4 7.0 - - - -
131j GLY 4.1 10.8 - - - +
132j VAL 3.5 3.4 - - - +
133j SER* 3.2 42.4 - - - +
152j PRO* 3.5 25.8 - - + -
164j ILE* 4.7 5.2 - - + -
165j GLY* 3.6 22.0 - - - +
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Residues in contact with GLY 29 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25j MET 3.0 13.6 + - - -
26j GLU* 3.2 7.6 + - - -
27j ALA 3.2 1.2 - - - -
28j ILE* 1.3 78.0 - - - +
30j HIS* 1.3 63.3 + - - +
31j ALA 3.3 0.9 - - - -
165j GLY 4.4 9.0 - - - -
166j ASN* 3.1 32.0 - - - +
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Residues in contact with HIS 30 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15i SER* 4.4 12.1 + - - -
26j GLU* 3.7 32.9 + - - -
27j ALA* 3.1 11.3 + - - +
28j ILE 3.1 1.4 + - - -
29j GLY* 1.3 82.2 + - - +
31j ALA* 1.3 61.6 + - - +
50j ARG* 3.5 19.3 + - - -
166j ASN* 4.8 5.5 + - - -
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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