Contacts of the strand formed by residues 138 - 146 (chain B) in PDB entry 1ZMC
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 VAL 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B PRO* 4.3 12.8 - - + -
5B ILE* 3.1 14.8 + - - +
126B GLN* 3.7 32.5 - - + +
127B VAL 3.8 2.7 - - - -
128B THR* 4.0 19.7 - - + +
136B THR* 5.0 4.9 - - - +
137B GLN* 1.3 95.4 + - - +
139B ILE* 1.3 69.6 + - - +
140B ASP* 4.4 9.9 - - - +
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Residues in contact with ILE 139 (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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5B ILE* 3.3 18.4 - - + +
7B ALA* 4.6 4.7 - - + -
10B THR* 3.5 24.7 - - + +
33B VAL* 3.8 27.8 - - + -
35B ILE* 3.6 29.6 - - + -
115B VAL* 4.0 15.7 - - + -
126B GLN* 3.1 4.4 - - - -
127B VAL* 2.8 46.5 + - + +
129B ALA* 5.2 1.1 - - + -
137B GLN* 4.3 7.4 - - + +
138B VAL* 1.3 84.9 - - - +
140B ASP* 1.3 72.3 + - - +
141B THR* 3.8 1.4 + - - +
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Residues in contact with ASP 140 (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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5B ILE 3.1 11.4 + - - +
6B ASP* 3.4 9.9 - - + +
7B ALA 2.8 26.5 + - - +
125B ASN* 3.2 13.2 - - - +
126B GLN* 3.6 17.2 + - - +
138B VAL* 4.4 10.0 - - - +
139B ILE* 1.3 73.8 - - - +
141B THR* 1.3 62.2 + - - +
161D ASP* 5.4 11.2 - - - +
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Residues in contact with THR 141 (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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7B ALA 3.0 9.0 - - - -
8B ASP 2.8 30.8 + - - -
10B THR* 3.1 28.6 + - - +
125B ASN* 2.6 47.1 + - - +
126B GLN 4.7 0.2 - - - +
127B VAL* 4.7 2.7 - - + -
139B ILE 4.4 4.9 - - - +
140B ASP* 1.3 76.1 - - - +
142B LYS* 1.3 59.6 + - - +
143B ASN 2.8 20.1 + - - +
144B ILE* 3.9 17.0 - - + -
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Residues in contact with LYS 142 (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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7B ALA 3.8 11.2 + - - +
8B ASP* 2.9 38.8 - - - +
125B ASN* 3.4 9.8 + - - +
141B THR* 1.3 77.4 + - - +
143B ASN* 1.3 71.7 + - - +
314B ASN* 2.8 29.6 + - - +
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Residues in contact with ASN 143 (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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8B ASP 3.0 15.6 + - - +
9B VAL* 4.4 6.0 - - + +
10B THR 3.1 14.5 + - - -
30B PHE* 5.3 6.1 - - - -
141B THR* 2.8 18.4 + - - +
142B LYS* 1.3 93.4 - - - +
144B ILE* 1.3 62.3 + - - +
314B ASN* 3.2 22.1 - - - +
316B TYR* 3.9 16.5 + - + -
342B MET* 4.3 29.6 - - + +
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Residues in contact with ILE 144 (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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10B THR 3.5 6.5 - - - +
12B ILE* 3.9 27.1 - - + -
121B ILE* 4.0 24.9 - - + -
123B GLY 3.9 19.5 - - - +
124B LYS 4.0 10.3 - - - +
126B GLN 4.1 1.6 - - - +
127B VAL* 3.7 27.6 - - + -
141B THR* 3.9 9.2 - - + -
143B ASN* 1.3 77.8 - - - +
145B LEU* 1.3 59.5 + - - +
146B ILE* 4.0 2.9 - - + -
314B ASN* 2.9 7.7 + - - +
315B ILE* 3.2 22.4 - - + -
316B TYR* 2.7 35.4 + - - +
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Residues in contact with LEU 145 (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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9B VAL* 4.8 4.7 - - + -
10B THR 2.9 12.8 + - - +
11B VAL* 3.3 16.7 - - + +
12B ILE 3.0 26.3 + - - -
21B ALA* 3.5 32.3 - - + -
143B ASN 4.2 0.2 - - - -
144B ILE* 1.3 73.3 - - - +
146B ILE* 1.3 61.5 + - - +
147B ALA* 3.5 0.9 + - + -
316B TYR* 3.3 31.2 - - + +
317B ALA* 4.0 0.7 - - - +
318B ILE* 4.0 26.0 - - + -
335B GLY 5.0 1.1 - - - +
338B CYS* 3.9 13.5 - - - -
339B VAL* 4.2 5.8 - - + -
342B MET* 4.2 20.6 - - + -
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Residues in contact with ILE 146 (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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12B ILE* 4.4 11.2 - - + -
121B ILE* 3.9 20.2 - - + -
144B ILE* 4.6 0.9 - - + -
145B LEU* 1.3 71.6 - - - +
147B ALA* 1.3 57.8 + - - +
148B THR* 3.4 26.0 - - + +
287B LEU* 3.6 16.8 - - + -
289B LEU* 3.7 29.6 - - + -
302B ILE* 3.9 22.9 - - + -
310B THR* 5.1 3.1 - - + -
315B ILE* 4.0 14.8 - - + -
316B TYR 2.5 16.6 + - - +
317B ALA* 3.1 7.1 - - + +
318B ILE* 3.1 27.2 + - - +
321B VAL* 4.1 2.3 - - + +
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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