Contacts of the strand formed by residues 22 - 31 (chain A) in PDB entry 1MZW
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 GLN 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER* 3.5 2.2 + - - -
19A ILE 2.8 34.7 + - - +
20A GLY 3.2 3.1 - - - +
21A GLY* 1.3 78.6 - - - +
23A GLU* 1.3 77.3 + - - +
24A VAL* 3.4 13.3 - - + +
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Residues in contact with GLU 23 (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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16A ASP* 4.6 9.0 - - - +
17A VAL 3.7 10.1 - - - +
18A SER* 3.9 11.3 + - - +
21A GLY 4.0 4.4 + - - +
22A GLN* 1.3 83.9 + - - +
24A VAL* 1.3 62.3 + - - +
25A GLY 3.7 3.5 + - - +
172A SER* 3.4 33.9 + - - -
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Residues in contact with VAL 24 (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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17A VAL* 2.9 32.1 + - + +
19A ILE* 3.9 38.1 - - + -
22A GLN* 3.4 25.4 - - + +
23A GLU* 1.3 75.3 - - - +
25A GLY* 1.3 58.3 + - - +
150A VAL* 3.7 11.3 - - + +
153A LYS* 2.7 49.4 + - + +
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Residues in contact with GLY 25 (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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15A PHE 3.9 0.3 - - - +
16A ASP* 3.6 4.0 - - - -
17A VAL* 3.0 29.0 + - - +
23A GLU* 3.7 3.6 - - - +
24A VAL* 1.3 81.5 - - - +
26A ARG* 1.3 60.7 + - - -
150A VAL* 3.6 10.9 - - - +
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Residues in contact with ARG 26 (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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14A PHE* 3.4 31.8 - - + -
15A PHE 3.4 5.2 - - - +
16A ASP* 2.7 41.2 + - - +
25A GLY* 1.3 72.5 - - - -
27A MET* 1.3 73.5 + - - +
28A LYS* 4.1 20.9 - - + +
146A ASP* 3.9 5.1 - - - +
147A GLY* 3.5 18.9 + - - -
150A VAL* 3.7 4.1 - - - +
173A GLN* 5.4 0.6 - - - +
177A MET* 4.5 6.5 - - - +
115B GLY 5.8 0.2 + - - -
117B PRO* 3.7 26.5 - - - +
120B LEU* 5.8 1.2 - - - +
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Residues in contact with MET 27 (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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14A PHE* 3.0 5.5 - - - +
15A PHE* 2.9 61.4 + - + +
17A VAL* 4.7 2.0 - - + -
26A ARG* 1.3 72.8 - - - +
28A LYS* 1.3 61.8 + - - +
29A ILE* 4.1 11.3 + - + +
65A PHE* 4.6 6.5 - - + -
126A ILE* 3.6 26.5 - - + -
144A ILE* 4.1 13.0 - - + -
146A ASP 3.3 6.7 - - - +
147A GLY* 3.7 5.4 - - - +
150A VAL* 3.4 30.7 - - + -
151A MET* 4.0 31.0 - - - -
154A ILE* 4.3 5.4 - - - -
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.3 4.9 - - + -
13A VAL 3.2 6.1 - - - +
14A PHE* 4.2 10.8 - - + -
26A ARG* 4.1 20.0 - - + +
27A MET* 1.3 76.7 - - - +
29A ILE* 1.3 60.1 + - - +
144A ILE* 3.5 5.4 - - - -
145A ILE* 2.8 44.7 + - + -
146A ASP* 2.8 34.2 + - + +
177A MET* 3.8 33.8 - - + +
115B GLY 4.9 4.6 + - - -
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.2 6.2 - - - +
13A VAL* 2.7 49.2 + - + +
14A PHE* 5.9 0.2 - - - -
15A PHE* 4.3 28.3 - - + +
27A MET* 4.3 15.3 - - + +
28A LYS* 1.3 80.1 - - - +
30A GLU* 1.3 72.7 + - - +
31A LEU* 3.7 13.4 + - + -
43A PHE* 4.7 6.7 - - + -
110A LEU* 3.8 45.5 - - + -
143A LYS 3.5 12.6 - - - +
144A ILE* 4.5 8.7 - - + -
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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
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10A ASN* 2.9 42.5 + - + +
11A PRO 3.4 7.0 - - - +
12A VAL* 4.4 11.9 - - + +
29A ILE* 1.3 73.4 - - - +
31A LEU* 1.3 62.3 + - - +
32A PHE* 3.6 18.2 + - + -
142A GLY* 3.1 6.4 - - - -
143A LYS* 2.9 46.4 + - + +
145A ILE* 3.8 21.1 - - + +
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Residues in contact with LEU 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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10A ASN* 3.3 16.9 - - - +
11A PRO* 2.8 27.3 + - + +
13A VAL* 3.9 20.0 - - + -
29A ILE* 3.9 19.1 - - + -
30A GLU* 1.3 72.6 - - - +
32A PHE* 1.3 54.0 + - - +
33A ALA 2.7 17.7 + - - -
40A ALA* 3.4 35.9 - - + +
43A PHE* 3.7 21.5 - - + -
44A ARG* 3.6 29.2 - - + +
141A PHE* 3.7 21.8 - - + +
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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