Contacts of the helix formed by residues 11 - 29 (chain B) in PDB entry 5IJ0
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 GLN 11 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLY* 1.3 81.4 - - - +
12B CYS* 1.3 65.1 + - - +
14B ASN* 2.9 23.9 + - - +
15B GLN* 2.9 21.5 + - - +
67B ASP* 2.9 25.7 + - - +
69B GLU* 5.4 8.0 - - + +
72B THR* 4.2 13.6 - - - +
143B THR* 3.5 19.4 + - - -
144B GLY* 4.0 3.8 + - - -
501B GDP 2.3 73.1 + - + +
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Residues in contact with CYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY 3.3 1.3 + - - -
11B GLN* 1.3 79.3 - - - +
13B GLY* 1.3 60.9 + - - +
15B GLN* 3.6 13.5 + - - -
16B ILE* 2.8 50.5 + - + +
137B HIS* 3.8 13.0 - - - -
138B SER* 3.6 31.0 - - - -
169B VAL* 4.0 6.5 - - - -
501B GDP 3.3 39.4 + - + +
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.7 8.0 - - - +
9B ALA 3.2 12.6 - - - -
10B GLY 3.3 4.4 + - - -
11B GLN 3.1 1.2 - - - -
12B CYS* 1.3 82.8 - - - +
14B ASN* 1.3 56.6 + - - +
17B GLY* 2.8 27.0 + - - -
136B THR* 3.2 35.3 - - - +
137B HIS* 4.4 0.9 - - - +
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.2 31.3 - - - +
9B ALA 2.9 16.7 + - - +
10B GLY* 3.5 21.0 - - - -
11B GLN 2.9 7.6 + - - +
13B GLY* 1.3 73.1 - - - +
15B GLN* 1.3 55.6 + - - +
17B GLY 3.3 0.2 + - - -
18B ALA* 2.7 34.0 + - - +
65B LEU* 4.0 9.6 - - + +
66B VAL 3.9 4.8 + - - -
67B ASP* 3.6 20.8 + - - +
72B THR* 4.3 10.4 - - + +
73B MET* 3.7 16.4 - - - +
76B VAL* 4.4 15.0 - - + +
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 2.9 19.0 + - - +
12B CYS* 3.6 5.7 + - - +
14B ASN* 1.3 72.2 - - - +
16B ILE* 1.3 66.5 + - - +
18B ALA* 2.9 18.2 + - - +
19B LYS* 3.0 17.1 + - - +
72B THR* 4.4 17.4 + - + +
76B VAL* 5.5 3.6 - - + -
226B ASN* 4.2 6.5 - - - +
501B GDP 2.8 45.2 + - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B CYS* 2.8 48.8 + - + +
15B GLN* 1.3 73.6 - - - +
17B GLY* 1.3 51.6 + - - +
19B LYS* 3.3 2.3 + - - +
20B PHE* 2.7 35.5 + - + +
136B THR* 3.7 23.1 - - + -
169B VAL* 4.4 8.3 - - + -
226B ASN* 3.2 43.3 - - + +
229B VAL* 4.6 15.3 - - + -
230B SER* 4.6 1.0 - - - -
233B MET* 4.1 20.9 - - + -
501B GDP 4.1 10.8 - - - +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 3.9 7.9 - - - -
8B GLN* 3.4 23.1 - - - -
13B GLY 2.8 21.3 + - - -
14B ASN 3.6 0.2 - - - -
15B GLN 3.1 0.2 - - - -
16B ILE* 1.3 74.3 - - - +
18B ALA* 1.3 59.4 + - - +
20B PHE* 3.4 6.9 - - - +
21B TRP* 2.8 36.0 + - - -
136B THR* 4.6 0.9 - - - +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 4.0 1.0 + - - -
14B ASN 2.7 17.6 + - - +
15B GLN* 2.9 12.3 + - - +
17B GLY* 1.3 73.0 - - - +
19B LYS* 1.3 60.0 + - + +
21B TRP* 3.2 5.8 + - - +
22B GLU* 2.9 28.5 + - - +
76B VAL* 5.0 17.0 - - + -
81B PHE* 5.2 10.0 - - + +
85B PHE* 5.6 6.3 - - + -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN 3.0 15.5 + - - +
16B ILE 3.8 5.8 - - - +
18B ALA* 1.3 78.5 - - + +
20B PHE* 1.3 56.8 + - - +
22B GLU* 2.8 38.9 + - - +
23B VAL* 2.9 31.9 + - - +
223B GLY* 4.2 21.3 - - - +
226B ASN* 4.1 31.4 - - + +
227B HIS* 4.4 19.6 + - - -
230B SER* 4.2 4.5 - - - +
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Residues in contact with PHE 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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6B HIS* 3.3 25.6 - + + -
16B ILE* 2.7 22.7 + - + +
17B GLY* 3.4 6.5 - - - +
19B LYS* 1.3 75.0 - - - +
21B TRP* 1.3 59.1 + + - +
23B VAL* 3.1 5.4 + - - +
24B ILE* 2.9 58.1 + - + +
50B TYR* 4.0 13.9 - + - -
134B GLN* 3.3 29.2 - - - -
230B SER* 3.7 20.1 - - - -
233B MET* 3.4 45.3 - - + -
234B SER* 3.7 15.9 - - - -
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Residues in contact with TRP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 3.0 30.4 + + + -
8B GLN* 3.0 26.0 - - - +
17B GLY 2.8 22.4 + - - +
18B ALA 3.9 3.1 - - - +
20B PHE* 1.3 70.0 - - - +
22B GLU* 1.3 61.8 + - - +
24B ILE* 3.7 17.2 - - + +
25B SER* 2.8 29.8 + - - -
50B TYR* 3.2 47.8 - + + -
51B TYR* 3.8 20.0 + + - -
61B PRO* 3.3 27.1 - - + -
62B ARG 3.2 24.9 - - - -
63B ALA* 3.6 9.9 - - + +
81B PHE* 4.9 4.6 - - + -
84B LEU* 5.2 6.7 - - + +
85B PHE* 3.5 22.4 - + + -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA 2.9 13.2 + - - +
19B LYS* 2.8 47.7 + - - +
21B TRP* 1.3 76.3 - - - +
23B VAL* 1.3 60.2 + - + +
25B SER* 2.5 23.9 + - - -
26B ASP* 2.9 30.1 + - - +
81B PHE* 3.5 42.8 - - + -
227B HIS* 6.0 2.2 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 2.9 19.2 + - - +
20B PHE* 3.4 8.5 - - - +
22B GLU* 1.3 77.5 - - + +
24B ILE* 1.3 57.1 + - - +
26B ASP* 3.1 13.2 + - + +
27B GLU* 2.8 34.7 + - + +
227B HIS* 4.4 22.0 - - + +
230B SER* 3.5 22.9 - - - +
231B ALA* 4.5 6.3 - - + +
234B SER* 3.4 34.1 - - - +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 2.9 63.3 + - + +
21B TRP* 3.8 24.9 - - + +
23B VAL* 1.3 72.1 - - - +
25B SER* 1.3 61.6 + - - +
27B GLU* 3.1 9.1 + - + +
28B HIS* 3.0 34.3 + - + +
50B TYR* 4.0 22.2 - - + -
51B TYR* 3.4 30.3 - - + +
234B SER* 5.0 8.1 - - - -
241B ARG* 5.8 3.6 - - - +
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Residues in contact with SER 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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21B TRP 2.8 18.1 + - - -
22B GLU 2.5 18.7 + - - -
24B ILE* 1.3 72.2 - - - +
26B ASP* 1.3 61.8 + - - +
29B GLY* 3.0 7.1 + - - -
30B ILE* 2.7 51.7 + - - +
51B TYR* 3.7 13.0 - - - -
81B PHE* 3.3 27.6 - - - -
84B LEU* 4.7 6.3 - - - -
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 2.9 34.6 + - - +
23B VAL* 3.3 11.3 - - - +
25B SER* 1.3 80.4 + - - +
27B GLU* 1.3 60.4 + - - +
29B GLY* 3.3 3.9 + - - -
81B PHE* 5.4 2.4 - - - -
227B HIS* 6.0 1.6 - - - -
359B ARG* 2.7 52.3 + - + +
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Residues in contact with GLU 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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23B VAL* 2.8 31.7 + - + +
24B ILE* 3.3 13.0 - - - +
26B ASP* 1.3 76.3 - - - +
28B HIS* 1.3 59.2 + - + +
43B GLN* 3.3 16.5 + - - +
234B SER* 4.6 6.3 + - - -
241B ARG* 4.0 26.7 - - - +
242B PHE* 4.0 21.0 - - - -
318B ARG* 3.1 38.8 + - - -
356B ILE* 5.3 2.1 - - - +
357B PRO 5.3 0.3 - - - +
358B PRO* 4.5 6.5 - - - +
359B ARG* 4.3 8.8 + - - +
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Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.0 33.8 + - + +
27B GLU* 1.3 73.9 - - + +
29B GLY* 1.3 63.6 + - - +
30B ILE* 3.3 16.3 + - + +
36B TYR* 3.3 23.9 - - - -
42B LEU 4.8 0.7 - - - -
43B GLN* 2.7 46.0 + - - +
47B ILE* 3.9 26.5 - - + +
49B VAL* 5.1 2.1 - - + +
50B TYR* 5.2 0.8 - - - +
51B TYR* 4.5 5.7 - + + -
241B ARG* 3.4 52.0 + - + -
242B PHE* 4.7 5.4 - + - -
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER 3.0 6.5 + - - -
26B ASP* 3.3 7.2 + - - -
27B GLU 3.3 4.2 - - - -
28B HIS* 1.3 78.7 - - - +
30B ILE* 1.3 60.4 + - - +
36B TYR* 4.1 0.9 - - - -
37B VAL* 3.2 37.2 + - - +
38B GLY* 3.2 9.3 + - - -
43B GLN* 3.4 11.1 - - - +
359B ARG* 4.5 5.8 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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