Contacts of the strand formed by residues 5 - 12 (chain E) in PDB entry 1ZMD
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 ILE 5 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E GLN 4.1 5.8 - - - +
4E PRO* 1.3 79.1 - - - +
6E ASP* 1.3 72.9 + - - +
31E LYS* 6.0 0.7 - - - -
33E VAL* 4.0 16.4 - - + -
113E VAL* 5.3 10.8 - - + -
115E VAL* 5.4 5.6 - - + -
137E GLN* 3.3 27.6 - - + +
138E VAL 2.7 11.8 + - - +
139E ILE* 3.8 20.9 - - + -
140E ASP* 2.9 32.2 + - - +
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Residues in contact with ASP 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E PRO 4.3 0.6 + - - +
5E ILE* 1.3 81.2 - - - +
7E ALA* 1.3 68.7 + - - +
31E LYS* 3.2 31.3 - - - +
33E VAL* 5.1 0.3 - - - +
140E ASP* 3.5 12.8 - - - +
142E LYS* 5.5 6.4 - - - -
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Residues in contact with ALA 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ASP* 1.3 81.8 + - - +
8E ASP* 1.3 62.8 + - - +
9E VAL 4.1 2.5 - - - +
10E THR* 3.6 22.7 - - - +
31E LYS* 3.7 15.7 - - + +
33E VAL* 3.7 23.1 - - + -
139E ILE* 3.9 4.5 - - + -
140E ASP 3.0 7.9 + - - +
141E THR* 2.9 25.1 - - - -
142E LYS* 3.2 6.8 + - - +
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Residues in contact with ASP 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA* 1.3 73.2 - - - +
9E VAL* 1.3 60.4 - - - +
29E GLY 4.7 1.4 - - - +
30E PHE* 3.8 24.5 - - + -
31E LYS* 2.9 39.1 + - - +
141E THR* 3.4 1.1 - - - -
142E LYS* 2.8 41.0 + - + +
143E ASN* 3.0 37.0 + - - +
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Residues in contact with VAL 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA* 4.1 0.7 - - - +
8E ASP* 1.3 83.5 - - - +
10E THR* 1.3 65.3 + - - +
11E VAL* 3.9 21.8 - - + -
25E ALA* 4.2 10.8 - - + -
30E PHE* 3.6 28.0 - - + -
31E LYS 3.1 2.9 + - - +
32E THR* 3.4 13.9 - - + +
33E VAL 2.9 25.3 + - - +
143E ASN* 3.7 5.6 - - - +
145E LEU* 5.0 5.4 - - + -
339E VAL* 4.7 1.1 - - + -
342E MET* 3.3 42.8 - - + -
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Residues in contact with THR 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA* 3.6 4.7 - - - +
9E VAL* 1.3 74.8 - - - +
11E VAL* 1.3 64.2 + - - +
12E ILE* 3.8 1.9 + - + +
33E VAL* 3.3 14.2 - - + +
35E ILE* 4.1 23.1 - - + -
127E VAL* 4.2 23.3 - - + -
139E ILE* 3.5 16.2 - - + +
141E THR* 3.2 31.8 + - - +
143E ASN 3.0 9.5 + - - -
144E ILE* 3.7 4.9 - - - +
145E LEU 3.0 25.3 + - - +
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Residues in contact with VAL 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.9 21.3 - - + -
10E THR* 1.3 73.6 - - - +
12E ILE* 1.3 56.8 + - - +
13E GLY 3.5 8.6 + - - +
18E GLY* 3.5 36.8 - - - +
21E ALA* 4.6 0.9 - - + -
22E ALA* 4.2 22.0 - - - +
32E THR* 4.6 1.1 - - + -
33E VAL 2.6 15.2 + - - +
34E CYS* 3.1 8.2 - - + -
35E ILE* 2.7 33.8 + - - +
145E LEU* 3.4 26.2 - - + +
147E ALA* 4.4 4.9 - - + -
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Residues in contact with ILE 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E THR* 4.3 6.5 - - + +
11E VAL* 1.3 73.4 - - - +
13E GLY* 1.3 59.1 + - - +
35E ILE* 3.9 8.5 - - + -
119E GLY* 4.6 7.2 - - - -
121E ILE* 3.9 20.4 - - + +
127E VAL* 3.9 23.3 - - + -
144E ILE* 3.8 24.2 - - + -
145E LEU 2.9 12.3 + - - +
146E ILE* 4.6 5.8 - - + -
147E ALA 3.0 28.8 + - - -
148E THR* 3.4 12.4 + - + +
287E LEU* 4.0 13.5 - - + -
480E FAD 3.7 34.3 - - + +
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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