Contacts of the strand formed by residues 20 - 24 (chain N) 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 GLU 20 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70M TYR* 3.9 18.8 - - + -
71M PRO* 4.3 5.4 - - - -
91M PRO* 3.6 4.4 - - + +
92M ARG* 3.3 7.8 + - - +
93M SER* 2.5 54.5 + - - -
193M SER* 4.1 2.4 + - - -
194M PRO* 4.5 0.4 - - - +
18N ILE* 3.7 4.2 - - - +
19N GLN* 1.3 83.1 - - + +
21N SER* 1.3 69.6 + - - +
22N ILE* 3.2 23.2 - - + +
43N VAL 4.2 0.2 - - - -
44N HIS* 3.4 0.7 - - - -
45N THR* 3.1 54.1 + - - +
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Residues in contact with SER 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M GLN* 4.0 5.9 - - - +
68M ASP* 4.7 9.0 - - - +
71M PRO* 4.3 5.7 - - - +
137M PRO* 3.5 30.9 - - - +
138M ALA* 5.8 1.6 - - - +
18N ILE* 4.0 5.5 - - - +
20N GLU* 1.3 78.8 + - - +
22N ILE* 1.3 65.7 + - - +
23N LEU 3.7 2.1 + - - -
42N LEU* 4.2 11.7 - - - +
43N VAL 3.4 7.2 - - - -
44N HIS* 3.2 32.8 - - - -
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Residues in contact with ILE 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M GLN* 3.5 20.4 - - + +
70M TYR* 6.0 2.0 - - + -
81M PHE* 5.5 2.9 - - + -
93M SER* 4.0 2.0 - - - +
191M HIS* 3.4 54.3 - - + +
193M SER* 4.2 9.0 - - - -
20N GLU* 3.2 35.2 - - + +
21N SER* 1.3 74.1 - - - +
23N LEU* 1.3 63.3 + - - +
24N MET* 3.6 8.0 - - + +
42N LEU* 3.4 1.2 - - - -
43N VAL* 2.6 46.8 + - + +
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Residues in contact with LEU 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M GLN* 2.8 36.6 + - - +
141M ARG* 4.2 14.4 - - - +
170M ARG 5.6 0.7 + - - -
171M ASP* 4.2 15.1 + - + +
21N SER 3.7 2.0 + - - -
22N ILE* 1.3 69.9 - - - +
24N MET* 1.3 62.1 + - - +
25N LEU* 6.1 0.2 - - - -
28N GLU* 4.6 1.2 - - - +
40N ASP* 5.8 4.9 - - + -
41N ILE 3.2 8.3 - - - +
42N LEU* 3.4 20.6 - - + +
61N ASP* 6.1 0.9 - - - +
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Residues in contact with MET 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169M GLY* 5.1 1.1 - - - -
171M ASP 5.9 0.2 - - - +
191M HIS* 3.9 18.2 - - + +
193M SER* 5.0 8.1 - - - -
195M LEU* 4.2 12.8 - - - -
196M SER* 3.5 31.9 - - - +
22N ILE* 3.6 15.0 - - + +
23N LEU* 1.3 79.1 - - - +
25N LEU* 1.3 66.0 + - - +
28N GLU* 3.3 50.5 - - + +
29N VAL* 4.3 9.4 - - + -
40N ASP* 3.5 5.9 - - - +
41N ILE* 2.6 38.3 + - - +
43N VAL* 3.7 21.3 - - + -
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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