Contacts of the strand formed by residues 25 - 37 (chain A) in PDB entry 1JG0
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLN* 3.9 0.2 - - - -
18A LYS 3.0 12.8 - - - -
19A ASN* 3.7 10.3 + - - -
23A GLY 2.7 9.0 + - - -
24A THR* 1.3 72.7 - - - +
26A THR* 1.3 64.1 + - - +
209A TYR* 3.6 4.0 - - - -
210A SER* 2.7 43.9 + - - -
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR 3.4 0.9 - - - +
17A GLN* 3.3 9.0 + - - +
18A LYS* 2.8 46.3 + - - +
20A ASP* 5.3 2.9 + - - +
24A THR 4.4 3.8 - - - +
25A GLY* 1.3 81.2 - - - +
27A LEU* 1.3 61.2 + - - +
28A SER* 4.3 7.6 + - - -
205A ASP* 5.5 0.2 + - - -
207A HIS* 4.0 17.5 - - + +
208A LEU 3.4 9.9 - - - -
209A TYR* 3.5 29.4 - - + -
210A SER* 4.1 2.5 - - - +
126B ARG* 4.3 15.5 + - - +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.1 32.3 - - + +
12A LEU* 4.1 31.4 - - + +
15A GLY 4.1 9.0 - - - +
16A THR 3.2 2.0 - - - -
17A GLN* 3.3 40.8 - - + +
26A THR* 1.3 72.1 - - - +
28A SER* 1.3 58.9 + - - +
207A HIS* 3.3 0.6 - - - -
208A LEU* 2.9 33.7 + - + +
210A SER* 5.6 2.2 - - - +
213A MET* 4.5 15.7 - - + -
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.6 0.7 - - - -
15A GLY* 3.5 1.0 - - - -
16A THR* 2.8 43.0 + - - +
18A LYS* 4.3 13.2 - - - +
26A THR* 4.0 5.3 - - - -
27A LEU* 1.3 76.3 - - - +
29A ILE* 1.3 65.0 + - - +
205A ASP* 3.6 13.6 + - - -
206A THR 3.4 11.0 - - - -
207A HIS* 3.6 13.7 - - - -
153B TYR* 3.0 28.1 + - - -
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.0 26.2 - - + -
10A LYS* 4.2 23.8 - - + +
11A VAL* 4.0 14.4 - - + -
14A GLU* 4.1 11.4 - - + +
15A GLY* 3.7 23.8 - - - +
28A SER* 1.3 79.4 - - - +
30A PHE* 1.3 64.3 + - - +
31A GLY 4.6 4.3 - - - +
32A HIS* 4.2 14.8 - - + -
205A ASP* 3.8 2.9 - - - -
206A THR* 3.0 41.4 + - - +
35B ARG* 6.0 1.8 - - - +
153B TYR* 4.1 4.8 - - - -
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 1.3 76.2 - - - +
31A GLY* 1.3 62.3 + - - +
204A GLY* 3.4 30.7 - - - -
205A ASP* 3.6 2.9 - - + -
35B ARG* 3.0 29.4 + - - +
151B GLN* 3.4 39.9 - - + -
153B TYR* 3.4 56.8 - + + -
160B SER* 3.9 13.0 - - - -
161B CYS* 3.8 9.0 - - - -
162B GLN* 3.5 36.8 - - + -
200B VAL* 4.0 7.1 - - + +
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 5.8 0.7 - - - -
29A ILE* 4.2 6.1 - - - +
30A PHE* 1.3 73.6 - - - +
32A HIS* 1.3 64.3 + - - +
203A GLY 3.3 9.8 + - - -
204A GLY 3.0 13.3 + - - -
206A THR* 4.8 0.4 + - - -
33B GLN* 3.7 5.0 - - - +
35B ARG* 2.6 26.9 + - - -
162B GLN* 3.7 13.2 - - - -
200B VAL* 4.3 10.8 - - - -
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Residues in contact with HIS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN 5.3 0.9 - - - -
6A GLU* 5.6 0.6 - - - +
7A LEU* 3.7 44.2 + - + +
10A LYS* 3.9 27.7 - - + +
29A ILE* 4.2 11.0 - - + -
31A GLY* 1.3 74.9 - - - +
33A GLN* 1.3 89.6 + - - +
34A MET* 4.2 11.8 - - + +
201A TRP* 4.0 18.7 - - + -
202A THR* 3.3 3.6 - - - -
203A GLY 2.8 29.3 + - - -
206A THR* 4.4 6.1 - - - +
33B GLN* 3.3 12.8 + - - +
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A HIS* 1.3 90.6 + - - +
34A MET* 1.3 68.7 + - - +
35A ARG* 4.9 2.4 + - - -
162A GLN* 3.1 13.1 + - - -
200A VAL* 3.7 17.8 - - + +
201A TRP 3.2 7.4 - - - +
202A THR* 3.0 23.6 + - - +
31B GLY 3.6 3.3 - - - +
32B HIS* 3.2 47.4 + - - +
33B GLN* 3.5 20.1 + - + +
202B THR* 3.8 4.6 - - - +
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Residues in contact with MET 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 3.6 43.7 - - + +
4A TYR* 4.7 4.7 - - - -
7A LEU* 4.1 6.5 - - + -
32A HIS* 4.2 15.5 - - + -
33A GLN* 1.3 81.2 - - - +
35A ARG* 1.3 60.3 + - - +
36A PHE* 3.9 24.4 - - + -
174A LEU* 3.8 29.4 - - + -
178A ILE* 3.9 9.6 - - + -
199A PHE 3.9 0.3 - - - +
200A VAL* 3.3 4.5 - - - +
201A TRP* 2.8 57.4 + - + +
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Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 2.9 23.5 + - - +
33A GLN* 4.9 2.4 + - - -
34A MET* 1.3 78.0 - - - +
36A PHE* 1.3 64.9 + - - +
37A ASN* 4.1 2.1 + - + +
160A SER* 5.6 0.4 + - - -
198A ASP* 2.9 42.7 + - + +
199A PHE 3.5 3.1 - - - -
200A VAL* 3.5 21.4 - - + +
10B LYS* 5.4 6.3 - - - +
29B ILE* 6.1 1.0 - - - +
30B PHE* 2.9 23.4 + - - +
31B GLY* 2.8 30.9 + - - -
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Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CXM 3.6 26.2 - - + -
3A GLN* 3.4 33.7 - - + +
4A TYR 5.0 0.9 - - - -
34A MET* 3.9 32.8 - - + -
35A ARG* 1.3 73.8 - - - +
37A ASN* 1.3 61.7 + - - +
38A LEU* 3.1 10.8 + - + +
43A PRO* 3.8 28.3 - - + -
178A ILE* 3.7 33.4 - - + -
198A ASP* 3.3 2.6 - - - -
199A PHE* 2.8 62.5 + + + +
201A TRP* 4.4 5.2 - - + -
227A LEU* 6.2 1.6 - - + -
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 5.3 0.6 - - - +
35A ARG* 4.1 3.5 + - + +
36A PHE* 1.3 68.6 - - - +
38A LEU* 1.3 59.7 + - - +
39A GLN* 2.9 33.5 + - - +
40A ASP* 2.8 52.7 + - - +
41A GLY 4.0 3.1 + - - +
158A LYS* 5.1 5.7 + - - +
196A VAL 4.8 0.2 + - - -
197A GLY* 3.8 6.7 + - - -
198A ASP* 3.3 19.3 + - - +
227A LEU* 5.7 0.3 - - - +
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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