Contacts of the helix formed by residues 29 - 43 (chain A) in PDB entry 1CEZ
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 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 3.0 16.4 + - - -
27A HIS 2.7 12.5 + - - -
28A TYR* 1.3 75.9 - - - +
30A GLU* 1.3 58.3 + - - -
31A ARG 3.1 6.7 + - - -
32A LEU 3.5 0.2 + - - -
33A ALA* 3.0 27.4 + - - +
172A LYS 3.8 8.9 + - - -
175A GLY* 3.1 19.8 - - - -
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 4.4 9.7 - - + -
25A ALA* 4.2 6.6 - - + +
29A GLY* 1.3 69.6 - - - -
31A ARG* 1.3 63.7 + - + +
33A ALA* 4.1 9.6 - - - -
34A ARG* 3.1 40.3 + - - +
165A ASN* 3.0 25.1 + - - +
166A VAL* 3.0 44.2 + - + +
173A ARG* 2.6 48.9 + - + +
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Residues in contact with ARG 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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29A GLY 3.1 1.4 + - - -
30A GLU* 1.3 81.1 - - + +
32A LEU* 1.3 65.2 + - + +
34A ARG* 3.5 6.0 + - - +
35A GLU* 3.1 33.8 + - - +
173A ARG 4.6 2.7 + - - +
175A GLY* 5.8 0.2 - - - -
176A HIS* 3.4 43.2 + - + +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.2 12.3 + - + +
29A GLY 3.5 2.0 + - - -
31A ARG* 1.3 79.8 - - + +
33A ALA* 1.3 61.7 + - - +
35A GLU* 3.7 13.3 - - - +
36A GLN* 2.8 33.8 + - - +
176A HIS* 4.9 16.8 - - + +
183A MET* 3.4 41.1 - - + -
272A VAL* 3.2 35.8 - - + +
273A VAL* 3.8 12.0 - - + +
411A HIS* 5.6 0.4 - - + +
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Residues in contact with ALA 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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21A PHE* 4.1 11.4 - - + +
24A LEU* 3.6 43.5 + - + +
25A ALA* 3.6 7.9 - - + +
28A TYR* 5.1 0.4 - - - +
29A GLY 3.0 18.9 + - - +
30A GLU* 4.1 5.6 - - - -
32A LEU* 1.3 79.2 - - - +
34A ARG* 1.3 62.5 + - - +
36A GLN* 3.5 1.9 + - - +
37A LEU* 3.4 26.7 + - - +
273A VAL* 4.9 0.8 - - - +
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.8 17.4 - - + -
30A GLU* 3.1 34.4 + - - +
31A ARG* 3.5 6.0 + - - +
32A LEU 3.2 0.4 - - - -
33A ALA* 1.3 78.4 - - - +
35A GLU* 1.3 59.2 + - - +
37A LEU* 3.4 3.1 + - - +
38A ALA* 3.0 29.7 + - + +
162A PHE* 2.7 44.2 + - + +
163A LYS* 3.9 8.7 + - - +
164A LYS 3.8 2.2 + - - -
165A ASN* 2.8 43.2 - - - +
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Residues in contact with GLU 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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31A ARG* 3.1 19.9 + - - +
32A LEU* 3.7 13.8 - - + +
34A ARG* 1.3 81.7 - - - +
36A GLN* 1.3 57.4 + - - +
38A ALA* 3.8 5.4 - - - +
39A LEU* 2.9 34.0 + - + +
50A ARG* 5.7 7.4 - - - +
272A VAL* 3.0 21.6 - - + +
408A PHE* 5.3 0.2 - - - -
411A HIS* 2.7 36.7 - - - -
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Residues in contact with GLN 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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24A LEU* 4.0 20.2 - - + -
32A LEU 2.8 20.3 + - - +
33A ALA 4.0 4.0 - - - +
34A ARG 3.3 0.2 - - - -
35A GLU* 1.3 73.3 - - - +
37A LEU* 1.3 59.2 + - - +
39A LEU* 3.4 11.3 - - - +
40A GLU* 2.6 60.4 + - - +
270A PRO 5.0 0.7 - - - +
271A CYS* 3.2 29.1 - - - +
272A VAL* 2.8 35.6 - - + +
273A VAL* 3.8 18.9 - - + +
286A TYR* 4.3 0.3 - - - -
287A TRP* 4.4 3.1 - - + -
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Residues in contact with LEU 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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20A PRO* 4.4 3.4 - - + -
21A PHE* 3.7 43.1 - - + +
24A LEU* 4.2 14.6 - - + -
33A ALA 3.4 17.4 + - - +
34A ARG 4.1 0.4 - - - +
35A GLU 3.3 0.2 - - - -
36A GLN* 1.3 73.8 - - - +
38A ALA* 1.3 68.6 + - - +
40A GLU* 3.2 4.1 + - - +
41A HIS* 2.9 33.8 + - - +
158A GLU* 4.0 10.5 - - + +
162A PHE* 4.0 22.9 - - + -
287A TRP* 4.1 4.9 - - + -
288A ALA* 3.5 39.9 - - + +
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Residues in contact with ALA 38 (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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34A ARG* 3.0 20.7 + - + +
35A GLU* 3.8 5.6 - - - +
37A LEU* 1.3 76.8 - - - +
39A LEU* 1.3 62.3 + - - +
41A HIS* 3.3 13.7 + - - +
42A GLU* 3.4 18.7 + - - +
50A ARG* 4.1 29.1 - - - +
162A PHE* 4.1 20.8 - - + -
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Residues in contact with LEU 39 (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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35A GLU* 2.9 19.8 + - + +
36A GLN* 3.4 13.9 - - - +
38A ALA* 1.3 77.5 - - - +
40A GLU* 1.3 63.4 + - + +
42A GLU* 3.2 39.1 + - - +
43A SER* 4.3 2.1 + - - -
269A GLN* 3.5 29.3 - - + +
270A PRO 3.1 28.3 - - - +
272A VAL* 4.1 14.4 - - + -
407A LYS* 3.9 17.0 - - - +
408A PHE* 4.0 19.5 - - + -
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Residues in contact with GLU 40 (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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36A GLN* 2.6 40.4 + - - +
37A LEU* 3.2 5.3 + - - +
39A LEU* 1.3 77.8 - - + +
41A HIS* 1.3 63.3 + - - +
43A SER* 3.2 24.6 + - - -
44A TYR* 4.2 6.8 - - - -
286A TYR* 3.2 16.0 - - + +
287A TRP* 2.8 23.7 + - - +
288A ALA* 2.9 34.5 + - + +
291A ARG* 3.1 36.2 + - - +
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Residues in contact with HIS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 2.9 26.3 + - - +
38A ALA* 3.7 6.7 - - - +
39A LEU 3.2 0.6 - - - -
40A GLU* 1.3 73.6 - - - +
42A GLU* 1.3 56.1 + - - +
43A SER 2.9 6.3 - - - -
44A TYR* 2.9 26.7 + + - +
45A GLU* 3.1 16.3 + - + +
155A ARG* 3.1 49.7 + - + +
158A GLU* 2.7 32.7 + - + -
159A ALA* 3.9 5.8 - - - +
162A PHE* 3.5 29.4 - + + -
288A ALA* 4.1 10.9 - - + +
290A GLY 4.6 3.1 - - - -
291A ARG* 6.0 0.7 - - + -
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Residues in contact with GLU 42 (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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38A ALA 3.4 10.6 + - - +
39A LEU* 3.3 32.3 - - - +
40A GLU 3.2 0.8 - - - -
41A HIS* 1.3 76.1 - - - +
43A SER* 1.3 57.9 + - - +
44A TYR 3.1 2.0 - - - -
45A GLU 3.6 11.4 - - - +
46A MET* 5.7 0.9 - - - -
47A GLY 5.6 4.9 - - - +
50A ARG* 5.1 19.3 + - + +
116A TYR* 3.1 33.5 + - + +
120A LYS* 3.5 10.2 - - - -
265A SER* 4.0 5.9 + - - -
266A PRO 6.1 0.2 - - - -
269A GLN* 3.3 11.7 - - - +
407A LYS* 2.8 29.7 + - - -
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 4.7 1.9 + - - -
40A GLU* 3.2 16.3 + - - -
41A HIS 2.9 1.0 - - - -
42A GLU* 1.3 78.8 - - - +
44A TYR* 1.3 79.8 + - - +
116A TYR* 5.3 0.9 - - - -
117A ILE* 4.0 6.8 - - - +
120A LYS* 4.2 3.5 + - - +
144A ALA* 5.8 0.7 - - - +
266A PRO 5.0 1.0 + - - -
267A MET* 2.6 59.3 + - - +
269A GLN* 5.6 1.4 + - - +
291A ARG* 4.6 9.6 + - - -
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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