Contacts of the helix formed by residues 25 - 34 (chain B) in PDB entry 2ZHX
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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170A ARG* 4.0 38.6 - - + +
171A ASP* 5.3 9.6 - - + +
174A THR* 6.1 4.0 - - + -
23B LEU* 5.8 4.3 - - + -
24B MET* 1.3 78.8 - - - +
26B PRO* 1.4 78.0 - - + +
27B GLU* 4.2 10.3 - - + +
28B GLU* 2.9 22.0 + - + +
29B VAL* 3.2 11.2 + - - +
40B ASP* 3.4 26.0 - - - +
41B ILE 5.2 0.2 - - - -
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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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25B LEU* 1.4 86.0 - - + +
27B GLU* 1.3 64.6 + - + +
28B GLU 2.9 1.7 + - - -
29B VAL* 3.0 1.9 + - - +
30B GLU* 2.9 26.2 + - - +
36B LYS* 4.1 17.0 - - + -
37B PRO* 3.5 44.3 - - + +
38B GLU 4.8 2.7 - - - +
39B SER* 4.1 6.1 - - - -
40B ASP* 3.3 27.5 - - - +
50H SER 5.4 3.4 - - - +
51H THR* 5.7 8.1 - - - +
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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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170A ARG* 4.9 15.5 - - + +
25B LEU* 3.2 10.3 - - + -
26B PRO* 1.3 82.7 - - + +
28B GLU* 1.3 61.5 + - + +
30B GLU* 4.1 15.7 + - - +
31B GLU* 4.1 11.8 + - - +
36B LYS* 5.3 3.7 - - - +
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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
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169A GLY* 3.8 4.7 - - - -
170A ARG* 3.3 51.6 + - + +
171A ASP 4.5 1.2 + - - -
190A PRO* 4.7 6.8 - - - +
191A HIS 4.7 3.1 + - - -
195A LEU* 5.6 0.9 - - - +
196A SER* 5.8 3.3 - - - -
23B LEU 4.6 1.0 - - - +
24B MET* 3.3 42.7 - - + +
25B LEU* 2.9 36.2 + - + +
27B GLU* 1.3 73.9 - - + +
29B VAL* 1.3 63.3 + - - +
31B GLU* 4.0 11.1 + - - +
32B VAL* 4.1 13.7 - - - +
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Residues in contact with VAL 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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195A LEU* 4.5 13.9 - - + -
24B MET* 4.2 16.4 - - + -
25B LEU 3.8 11.2 - - - +
26B PRO 3.0 6.1 + - - +
28B GLU* 1.3 76.2 - - - +
30B GLU* 1.3 66.9 + - - +
32B VAL* 3.2 13.2 + - - +
33B ILE* 3.2 13.5 + - + +
37B PRO* 4.2 8.3 - - + -
41B ILE* 4.1 25.6 - - + -
58B LEU* 3.8 15.7 - - + -
68B TRP* 3.6 36.1 - - + -
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Residues in contact with GLU 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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26B PRO 2.9 14.7 + - - +
27B GLU* 4.2 11.5 - - - +
28B GLU 3.4 0.2 - - - -
29B VAL* 1.3 76.2 - - - +
31B GLU* 1.3 62.6 + - - +
32B VAL 3.0 0.5 + - - -
33B ILE 3.1 0.2 + - - -
34B GLY* 2.5 37.8 + - - -
35B ASN 4.1 13.7 - - - +
36B LYS* 3.4 48.2 + - + +
37B PRO* 4.4 0.2 - - - +
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Residues in contact with GLU 31 (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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199A ARG* 3.1 45.5 + - - +
27B GLU 4.1 8.3 + - - +
28B GLU* 4.0 10.4 + - - +
29B VAL 3.5 0.2 - - - -
30B GLU* 1.3 82.8 - - - +
32B VAL* 1.3 60.3 + - - +
34B GLY* 4.2 3.1 + - - -
59E ASN* 3.1 33.5 + - - +
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Residues in contact with VAL 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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195A LEU* 3.4 47.8 - - + +
196A SER* 4.9 2.2 - - - -
199A ARG* 3.7 31.9 - - + +
28B GLU 4.1 14.1 - - - +
29B VAL 3.2 6.1 + - - +
30B GLU 3.1 0.8 - - - -
31B GLU* 1.3 77.2 - - - +
33B ILE* 1.3 61.7 + - + +
79B ASN* 4.0 21.8 + - - +
81B ILE* 3.7 10.5 - - + +
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Residues in contact with ILE 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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195A LEU* 4.4 11.7 - - + -
29B VAL* 3.2 12.2 + - + +
30B GLU 3.1 1.2 + - - -
32B VAL* 1.3 78.6 - - + +
34B GLY* 1.3 61.6 + - - +
35B ASN* 4.2 11.3 - - + +
58B LEU* 3.7 30.3 - - + -
68B TRP* 3.8 16.2 - - + -
69B ALA* 4.3 5.8 - - + -
71B VAL* 4.0 17.3 - - + -
81B ILE* 3.5 38.3 - - + +
83B MET* 3.8 20.9 - - - -
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Residues in contact with GLY 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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30B GLU* 2.5 25.5 + - - -
31B GLU 4.2 3.3 + - - -
32B VAL 3.6 1.2 - - - -
33B ILE* 1.3 75.3 - - - +
35B ASN* 1.3 68.8 + - - +
36B LYS 4.2 0.9 - - - -
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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