Contacts of the strand formed by residues 26 - 37 (chain B) 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 THR 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ARG* 4.3 5.3 + - - +
16B THR 3.3 2.1 - - - +
17B GLN* 3.5 8.3 + - - +
18B LYS* 3.0 35.3 + - - +
20B ASP* 3.1 18.7 + - - +
25B GLY* 1.3 81.5 - - - +
27B LEU* 1.3 61.8 + - - +
28B SER* 4.5 5.5 + - - -
205B ASP* 5.6 0.2 + - - -
207B HIS* 4.0 20.6 - - + +
208B LEU 3.4 9.6 - - - +
209B TYR* 3.3 37.9 - - + -
210B SER* 4.3 2.2 - - - -
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Residues in contact with LEU 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 29.9 - - + +
12B LEU* 4.1 23.1 - - + +
15B GLY* 4.1 8.5 - - - +
16B THR 3.3 2.9 - - - +
17B GLN* 3.2 43.5 - - + +
26B THR* 1.3 72.3 - - - +
28B SER* 1.3 61.2 + - - +
207B HIS* 3.1 4.0 - - - +
208B LEU 2.9 29.9 + - - +
210B SER* 5.7 0.2 - - - +
213B MET* 3.5 29.8 - - + -
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 2.8 33.6 + - - -
11B VAL* 4.6 0.9 - - - -
14B GLU 4.6 0.3 - - - +
15B GLY* 3.3 3.8 - - - -
16B THR* 2.9 35.4 + - - +
18B LYS* 4.3 11.6 - - - +
26B THR* 4.5 5.6 - - - -
27B LEU* 1.3 76.3 - - - +
29B ILE* 1.3 65.5 - - - +
205B ASP* 3.5 23.5 + - - -
206B THR 3.4 6.7 - - - -
207B HIS* 3.6 5.6 - - - -
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Residues in contact with ILE 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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35A ARG* 6.1 0.7 - - - +
153A TYR* 4.1 5.4 - - - -
7B LEU* 4.0 26.0 - - + -
10B LYS* 4.3 17.7 - - + +
11B VAL* 4.1 15.7 - - + -
14B GLU* 4.1 12.1 - - + +
15B GLY* 3.8 20.9 - - - +
28B SER* 1.3 82.0 - - - +
30B PHE* 1.3 62.3 + - - +
31B GLY 4.7 3.8 - - - +
32B HIS* 4.1 21.5 - - + -
204B GLY 3.4 0.2 - - - +
205B ASP* 3.7 3.5 - - - -
206B THR* 2.9 45.8 + - - +
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Residues in contact with PHE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 2.9 30.6 + - - +
151A GLN* 3.4 38.8 - - + -
153A TYR* 3.4 54.2 - + + -
160A SER* 3.9 12.6 - - - -
161A CYS 3.7 12.1 - - - -
162A GLN* 3.5 36.1 - - + -
200A VAL* 4.1 7.1 - - + +
29B ILE* 1.3 76.9 - - - +
31B GLY* 1.3 60.5 + - - +
204B GLY* 3.3 30.3 - - - -
205B ASP* 3.7 1.1 - - + -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 3.6 8.3 - - - +
35A ARG* 2.8 23.7 + - - -
162A GLN* 3.7 16.4 - - - -
200A VAL* 4.4 5.2 - - - -
10B LYS* 5.2 1.6 + - - -
29B ILE* 4.2 5.1 - - - +
30B PHE* 1.3 73.6 - - - +
32B HIS* 1.3 67.6 + - - +
203B GLY 3.1 10.7 + - - -
204B GLY 3.0 14.1 + - - -
206B THR* 4.7 0.4 + - - -
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 3.2 14.6 + - - +
3B GLN 5.2 0.9 - - - -
6B GLU* 5.7 0.6 - - + -
7B LEU* 3.5 39.6 + - + +
10B LYS* 3.6 37.4 + - + +
29B ILE* 4.1 11.2 - - + -
31B GLY* 1.3 74.8 - - - +
33B GLN* 1.3 76.0 + - - +
34B MET* 3.6 27.6 - - + +
201B TRP* 4.2 14.7 - - + -
202B THR* 3.3 3.8 - - - -
203B GLY 2.9 27.0 + - - -
206B THR* 4.5 5.8 - - - +
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Residues in contact with GLN 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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31A GLY 3.7 3.5 - - - +
32A HIS* 3.3 46.3 + - - +
33A GLN* 3.5 17.2 + - + +
202A THR* 3.7 4.9 - - - +
3B GLN* 4.9 0.3 - - - +
32B HIS* 1.3 86.6 + - - +
34B MET* 1.3 72.0 + - - +
35B ARG* 4.8 2.6 + - + -
162B GLN* 3.0 13.1 + - - -
200B VAL* 3.7 17.6 - - + +
201B TRP 3.1 6.7 - - - +
202B THR* 2.9 24.2 + - - +
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Residues in contact with MET 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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3B GLN* 3.4 46.0 - - + +
4B TYR* 4.2 2.9 - - - -
7B LEU* 4.0 11.7 - - + -
32B HIS* 3.6 14.4 - - + +
33B GLN* 1.3 80.8 - - - +
35B ARG* 1.3 61.8 + - - +
36B PHE* 3.9 17.9 - - + -
174B LEU* 3.9 24.0 - - + -
178B ILE* 4.1 17.9 - - + -
200B VAL* 3.4 6.1 - - - +
201B TRP* 2.8 57.9 + - + +
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Residues in contact with ARG 35 (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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10A LYS* 5.8 5.9 - - - +
29A ILE* 6.0 1.8 - - - +
30A PHE* 3.0 21.0 + - - +
31A GLY* 2.6 32.5 + - - -
3B GLN* 2.4 41.6 + - - +
33B GLN* 4.8 4.2 + - + -
34B MET* 1.3 75.2 - - - +
36B PHE* 1.3 62.0 + - - +
37B ASN 4.1 1.9 + - - +
160B SER* 5.8 0.2 + - - -
198B ASP* 3.1 40.3 + - + +
199B PHE 3.6 2.5 - - - -
200B VAL* 3.4 21.3 - - + +
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CXM 3.8 27.8 - - + -
3B GLN* 4.0 18.4 - - + -
4B TYR* 5.1 1.6 - - + -
34B MET* 3.9 37.5 - - + -
35B ARG* 1.3 76.2 - - - +
37B ASN* 1.3 61.9 + - - +
38B LEU* 3.1 16.0 + - + +
43B PRO* 3.9 23.8 - - + -
178B ILE* 4.1 32.3 - - + -
198B ASP* 3.2 3.4 - - - -
199B PHE* 2.7 60.8 + + + +
201B TRP* 4.6 5.2 - - + -
227B LEU* 6.1 2.0 - - + -
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Residues in contact with ASN 37 (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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35B ARG* 4.1 3.4 + - - +
36B PHE* 1.3 68.2 - - - +
38B LEU* 1.3 59.2 + - - +
39B GLN* 3.1 26.8 + - - +
40B ASP* 2.9 50.0 + - - +
41B GLY 4.0 3.6 + - - +
196B VAL 4.7 0.3 - - - +
197B GLY* 3.8 5.2 - - - +
198B ASP* 3.4 19.7 + - - +
227B LEU* 5.8 0.2 - - - +
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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