Contacts of the helix formed by residues 25 - 37 (chain B) in PDB entry 2ZZA
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 LEU 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B TRP* 4.0 13.2 - - + -
24B HIS* 1.3 82.0 + - - +
26B PRO* 1.3 68.6 - - - +
28B GLU* 2.8 26.1 + - + +
29B LEU* 3.1 17.0 + - - +
117B ILE* 3.8 42.6 - - + -
149B ASN* 3.1 33.9 - - + +
150B PRO* 3.9 2.2 - - + -
151B HIS* 3.7 29.6 - - + +
153B TYR* 4.1 16.6 - - + -
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Residues in contact with PRO 26 (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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24B HIS* 3.5 34.0 - - + +
25B LEU* 1.3 85.7 - - - +
27B ALA* 1.3 61.1 + - - +
29B LEU* 3.2 11.3 + - + +
30B GLN* 3.2 25.8 + - - +
148B LYS* 3.2 26.2 - - + +
149B ASN* 3.0 12.6 - - - +
164B FOL 5.3 1.8 - - - +
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Residues in contact with ALA 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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26B PRO* 1.3 75.5 - - - +
28B GLU* 1.3 61.3 + - - +
30B GLN* 3.4 11.6 + - - +
31B LEU* 3.2 17.7 + - - +
143B TYR* 6.1 0.4 - - + -
146B ASP* 5.7 0.7 - - - +
149B ASN* 2.8 31.0 + - - +
153B TYR* 3.5 17.7 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 3.7 7.0 - - + +
23B TRP* 5.1 3.2 + - - +
25B LEU* 2.8 30.6 + - + +
27B ALA* 1.3 76.3 - - - +
29B LEU* 1.3 60.6 + - - +
30B GLN 3.1 0.4 - - - -
31B LEU* 2.9 23.5 + - + +
32B PHE* 2.9 10.7 + - - +
115B THR* 2.9 44.7 + - + -
117B ILE* 5.2 1.1 - - + -
149B ASN* 4.1 0.4 + - - -
153B TYR* 3.6 21.4 + - + -
164B FOL 2.6 43.2 + - - +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 5.4 3.6 - - + -
24B HIS* 4.9 19.1 - - + +
25B LEU 3.1 14.8 + - - +
26B PRO* 3.2 9.4 + - + +
28B GLU* 1.3 76.4 - - + +
30B GLN* 1.3 58.3 + - - +
32B PHE* 3.2 9.3 + - + +
33B LYS* 2.9 26.9 + - - +
164B FOL 3.2 96.6 - - + +
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Residues in contact with GLN 30 (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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91A GLU* 3.5 33.2 + - - +
26B PRO 3.2 15.1 + - - +
27B ALA* 3.5 11.9 - - - +
28B GLU 3.1 0.6 - - - -
29B LEU* 1.3 77.5 - - - +
31B LEU* 1.3 60.5 + - - +
33B LYS* 3.6 17.9 - - - +
34B ARG* 2.9 28.4 + - - +
164B FOL 4.5 16.2 - - - +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A 1PE 4.0 15.4 - - - +
6B ILE* 4.8 8.3 - - + -
27B ALA 3.2 10.9 + - - +
28B GLU* 2.9 16.0 + - - +
30B GLN* 1.3 75.7 - - - +
32B PHE* 1.3 68.2 + - - +
34B ARG* 3.2 12.0 + - - +
35B ALA* 2.9 21.2 + - + +
115B THR* 4.0 12.6 - - - +
143B TYR* 4.2 23.8 - - + +
153B TYR* 4.4 11.7 - - + +
155B PHE* 3.8 48.9 - - + -
164B FOL 4.9 0.2 - - - +
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Residues in contact with PHE 32 (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 ILE* 3.8 17.9 - - + -
28B GLU 2.9 12.0 + - - +
29B LEU* 3.3 11.7 - - + +
31B LEU* 1.3 77.9 - - - +
33B LYS* 1.3 59.9 + - - +
35B ALA* 3.2 2.8 + - - +
36B THR* 2.8 38.7 + - + +
41B ILE* 5.2 0.9 - - + -
55B LEU* 3.6 32.5 - - + -
58B ARG* 3.9 6.1 - - - -
96B ILE* 3.4 40.2 - - + -
164B FOL 3.4 81.9 - + + +
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Residues in contact with LYS 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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91A GLU* 3.0 44.2 + - - +
29B LEU 2.9 17.9 + - - +
30B GLN* 3.6 19.3 - - - +
32B PHE* 1.3 77.2 - - - +
34B ARG* 1.3 57.1 + - - +
36B THR* 3.6 5.6 - - - -
37B LEU* 2.7 62.2 + - + +
56B PRO* 6.1 3.1 - - - -
58B ARG* 3.7 15.9 - - - +
164B FOL 3.4 29.8 - - + +
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Residues in contact with ARG 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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34A ARG 5.5 1.9 - - - +
39A LYS* 6.4 0.2 - - - +
113A TYR* 6.0 0.4 - - - -
139A GLU* 2.6 44.8 + - - -
157A LEU* 5.1 4.4 - - - +
165A 1PE 3.2 91.4 + - - +
30B GLN 2.9 19.7 + - - +
31B LEU* 3.4 9.1 - - - +
33B LYS* 1.3 79.0 - - - +
35B ALA* 1.3 60.0 + - - +
36B THR 3.5 0.3 + - - -
37B LEU* 4.1 10.9 + - - +
39B LYS* 5.8 0.5 - - - -
143B TYR* 4.7 4.4 + - - -
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Residues in contact with ALA 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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165A 1PE 3.8 18.2 - - - +
6B ILE* 3.8 16.8 - - + -
31B LEU* 2.9 18.7 + - + +
34B ARG* 1.3 76.9 - - - +
36B THR* 1.3 60.0 + - - +
39B LYS* 2.8 28.7 + - - +
94B MET* 3.3 7.7 - - + +
113B TYR* 3.8 28.9 - - + -
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Residues in contact with THR 36 (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 ILE* 4.2 4.7 - - + -
32B PHE* 2.8 47.3 + - + +
33B LYS 3.3 0.2 + - - -
35B ALA* 1.3 82.2 - - - +
37B LEU* 1.3 69.3 + - - +
38B GLY 3.2 0.2 + - - -
39B LYS* 2.9 25.8 + - - +
41B ILE* 3.9 15.5 - - + -
58B ARG* 3.0 37.8 + - - +
94B MET* 4.0 17.9 - - + -
96B ILE* 4.2 0.2 - - + -
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Residues in contact with LEU 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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37A LEU* 3.8 16.9 - - - +
38A GLY 3.8 16.4 - - - +
39A LYS* 3.6 38.8 - - + -
33B LYS* 2.7 47.0 + - + +
34B ARG* 4.1 9.2 + - - +
35B ALA 3.9 0.2 - - - -
36B THR* 1.3 75.2 + - - +
38B GLY* 1.3 63.7 + - - +
39B LYS* 3.2 10.2 + - - +
56B PRO 4.0 14.8 - - - +
57B GLY* 3.9 12.8 - - - +
58B ARG* 3.8 8.1 - - - +
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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