Contacts of the helix formed by residues 31 - 47 (chain B) in PDB entry 1GPU
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 PRO 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA 5.8 0.4 - - - +
20B VAL* 4.8 9.6 - - + +
23B VAL* 4.2 17.3 - - + -
29B GLY 3.5 6.3 - - - +
30B HIS* 1.3 83.1 - - - +
32B GLY* 1.3 69.3 + - - +
34B PRO* 3.2 8.3 - - + +
35B LEU* 3.2 28.9 + - + +
262B VAL* 3.4 13.0 - - + +
265B ALA 3.1 32.3 - - - +
267B LEU* 4.0 33.9 - - + +
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B HIS 3.5 1.2 - - - -
31B PRO* 1.3 77.8 - - - +
33B ALA* 1.3 62.2 + - - +
35B LEU 3.3 0.2 + - - -
36B GLY* 3.1 10.6 + - - -
250B ILE* 3.6 21.0 - - - +
251B GLY* 3.0 25.3 + - - -
262B VAL* 2.8 25.4 + - - -
263B HIS 4.1 1.9 + - - -
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B HIS* 5.2 0.6 - - - +
32B GLY* 1.3 68.8 - - - +
34B PRO* 1.3 68.6 - - + +
36B GLY* 3.1 1.5 + - - +
37B MET* 2.7 36.3 + - + +
67B ASN* 4.5 8.1 - - - +
69B HIS* 4.4 4.0 - - + +
70B ALA* 3.6 21.1 - - + -
185B ASP* 4.1 18.2 - - - +
187B ASN* 5.3 0.2 - - - +
250B ILE* 4.0 5.9 - - - +
263B HIS 5.2 1.8 + - - -
1682B THD 3.5 22.3 + - - +
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Residues in contact with PRO 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 4.8 1.4 - - - +
19B ALA* 3.9 22.0 - - + -
30B HIS* 3.2 25.1 - - + +
31B PRO* 3.2 13.9 - - + +
33B ALA* 1.3 94.5 - - + +
35B LEU* 1.3 62.2 + - + +
37B MET 3.9 0.3 - - - -
38B ALA* 3.1 26.2 + - - +
70B ALA* 3.8 25.6 - - + +
72B ALA* 4.4 3.6 - - + -
73B LEU* 3.8 29.1 - - + +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 2.9 61.4 + - + +
19B ALA* 6.3 0.2 - - + -
20B VAL* 3.6 31.0 - - + -
31B PRO* 3.2 18.5 + - + +
32B GLY 3.6 3.8 - - - +
34B PRO* 1.3 81.8 - - + +
36B GLY* 1.3 62.4 + - - +
38B ALA 3.8 2.1 + - - -
251B GLY* 3.6 30.1 - - - +
252B TYR* 3.6 20.8 - - - +
254B SER* 4.6 1.8 - - - -
267B LEU* 4.1 17.9 - - + -
275B LEU* 4.2 10.1 - - + -
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 4.7 0.7 + - - -
32B GLY 3.1 10.0 + - - -
33B ALA* 3.1 6.6 + - - -
35B LEU* 1.3 79.9 - - - +
37B MET* 1.3 61.4 + - - +
39B PRO* 3.7 9.2 - - - +
185B ASP* 5.2 0.9 - - - -
220B GLY 4.2 3.5 - - - +
221B ASN* 4.7 1.8 - - - +
246B MET* 4.8 0.5 - - - +
248B THR* 3.6 29.9 - - - +
249B THR 3.9 19.1 - - - -
250B ILE* 5.0 0.9 - - - -
251B GLY 4.3 0.8 - - - +
252B TYR* 4.6 2.7 - - - -
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Residues in contact with MET 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 2.7 20.8 + - - +
34B PRO 3.9 0.7 - - - -
36B GLY* 1.3 71.2 - - - +
38B ALA* 1.3 63.9 + - - +
39B PRO* 3.3 3.1 - - - -
40B ALA* 3.2 8.4 + - - +
41B ALA* 2.9 21.7 + - - +
65B LEU* 5.4 0.7 - - - -
67B ASN* 3.5 24.9 - - - +
70B ALA* 5.8 0.9 - - - -
73B LEU* 3.7 15.5 - - + -
154B PHE* 3.4 46.8 - - + -
155B LEU 4.8 0.4 - - - +
183B ILE* 4.0 11.4 - - + +
185B ASP* 3.5 39.7 - - + +
246B MET* 4.1 17.5 - - + -
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 4.1 7.2 - - + +
15B ILE* 3.9 20.2 - - + +
16B ARG* 3.4 31.2 - - + +
34B PRO 3.1 13.6 + - - +
35B LEU 4.0 0.4 - - - +
36B GLY 3.5 0.2 - - - -
37B MET* 1.3 76.1 - - - +
39B PRO* 1.3 70.9 - - + +
41B ALA* 3.1 2.8 + - - +
42B HIS* 3.0 23.6 + - - +
73B LEU* 4.2 10.1 - - - -
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Residues in contact with PRO 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.9 18.4 - - + -
16B ARG* 3.1 34.1 - - - +
35B LEU 4.2 0.2 - - - +
36B GLY 3.7 7.9 - - - +
37B MET 3.5 3.8 - - - -
38B ALA* 1.3 92.0 - - + +
40B ALA* 1.3 61.9 + - - +
42B HIS* 3.2 2.6 + - - +
43B VAL* 3.0 26.3 + - - +
220B GLY 3.7 15.5 - - - +
221B ASN 3.5 14.4 - - - +
222B GLU* 5.1 0.9 - - - +
224B LEU* 3.9 18.5 - - + +
227B ILE* 4.1 5.8 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B MET* 3.2 8.4 + - - +
39B PRO* 1.3 80.0 - - - +
41B ALA* 1.3 58.0 + - - +
43B VAL* 4.0 0.5 - - - +
44B LEU* 2.8 34.0 + - - +
154B PHE* 3.8 17.7 - - + -
183B ILE* 4.7 3.8 - - + -
220B GLY 5.1 0.2 + - - -
227B ILE* 3.8 19.4 - - + +
246B MET* 3.6 37.0 - - + -
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B MET 2.9 13.2 + - - +
38B ALA 3.4 8.3 - - - +
40B ALA* 1.3 77.6 - - - +
42B HIS* 1.3 56.9 + - - +
45B TRP* 2.9 41.0 + - + +
63B PHE* 6.2 0.2 - - + -
73B LEU* 3.9 28.3 - - + -
77B MET* 3.9 18.4 - - + -
154B PHE* 3.7 13.6 - - + -
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.6 4.8 - + - -
8B ASP* 2.8 45.0 + - + +
11B ALA* 3.7 15.0 - - + +
12B VAL* 3.9 17.7 - - + -
15B ILE* 3.9 7.6 - - + +
38B ALA 3.0 11.6 + - - +
39B PRO 3.7 6.7 - - - +
41B ALA* 1.3 76.4 - - - +
43B VAL* 1.3 67.5 + - + +
45B TRP* 4.1 0.3 - - - +
46B SER* 2.6 56.4 + - - -
77B MET* 4.2 8.7 - - - +
224B LEU* 4.9 1.8 - - + -
296B HIS* 4.2 7.6 - + - -
297B TYR* 2.7 32.0 + + - -
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Residues in contact with VAL 43 (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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4B PHE* 3.9 19.9 - - + -
39B PRO 3.0 16.0 + - - +
40B ALA 4.0 0.2 - - - +
42B HIS* 1.3 80.9 - - + +
44B LEU* 1.3 64.4 + - - +
46B SER* 3.3 9.5 + - - -
47B GLN* 3.3 15.6 + - + +
224B LEU* 3.7 36.1 - - + +
227B ILE* 3.8 15.9 - - + -
228B ALA* 3.7 38.1 - - + +
231B ILE* 4.2 5.2 - - + -
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Residues in contact with LEU 44 (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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40B ALA 2.8 22.6 + - - +
41B ALA 4.0 1.6 - - - +
43B VAL* 1.3 72.6 - - - +
45B TRP* 1.3 65.9 + - + +
47B GLN* 3.0 49.8 + - - +
48B MET* 3.2 11.8 + - + +
63B PHE* 3.7 30.7 - - + -
152B TYR* 3.4 38.4 - - + -
153B VAL 5.5 0.2 - - - +
154B PHE* 3.7 21.5 - - + -
183B ILE* 4.8 5.4 - - + -
231B ILE* 4.0 20.8 - - + +
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Residues in contact with TRP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA* 2.9 31.8 + - - +
42B HIS 4.3 0.7 - - - +
44B LEU* 1.3 86.7 - - + +
46B SER* 1.3 63.2 + - - +
47B GLN 3.2 0.9 + - - -
48B MET* 3.2 13.1 + - - +
50B MET* 3.0 41.7 - - + +
63B PHE* 3.7 40.1 - + + -
74B LEU* 3.6 23.1 - - + -
77B MET* 3.8 42.9 - - + +
78B LEU* 3.7 21.1 - - + -
81B THR* 3.6 28.0 - - + -
83B TYR* 3.8 16.8 - + - -
110B GLY 5.3 2.2 - - - -
301B ILE* 3.4 10.0 - - + +
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 5.3 7.2 - - - -
8B ASP* 5.7 0.7 - - - -
42B HIS* 2.6 51.3 + - - -
43B VAL* 3.7 6.3 - - - -
44B LEU 3.2 0.2 - - - -
45B TRP* 1.3 76.4 - - - +
47B GLN* 1.3 59.4 + - - +
48B MET 3.5 1.7 - - - +
296B HIS* 5.4 1.8 + - - -
297B TYR* 4.0 8.0 - - - -
300B THR* 4.1 23.7 + - - +
301B ILE* 3.8 11.5 - - - +
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.3 14.7 + - + +
44B LEU* 3.0 41.5 + - - +
46B SER* 1.3 76.3 - - - +
48B MET* 1.3 64.3 + - - +
49B ARG* 3.8 1.7 + - - +
61B ASP* 4.4 2.6 - - - +
152B TYR* 3.2 21.3 + - - -
228B ALA* 6.3 0.9 - - - -
231B ILE* 3.7 16.2 - - + +
235B LYS* 2.9 36.0 + - - -
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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