Contacts of the strand formed by residues 19 - 25 (chain A) in PDB entry 1ZM9
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU 4.2 9.2 - - - +
13A MET* 5.0 0.2 - - - -
15A LYS 3.6 13.7 - - - +
16A VAL* 3.0 17.8 + - + +
18A ASN* 1.3 83.0 - - - +
20A ARG* 1.3 82.4 + - - +
21A ASN* 3.7 12.1 - - - +
99A LEU* 3.0 22.4 - - + +
101A ASN* 3.6 17.5 - - - +
344A SER* 3.3 1.7 - - - -
345A PRO* 3.1 29.3 - - + +
451A GLY 4.2 4.7 - - - +
452A ASN* 4.3 17.0 - - - +
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Residues in contact with ARG 20 (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 THR 3.4 19.2 + - - -
18A ASN 3.9 2.4 - - - -
19A VAL* 1.3 105.8 + - - +
21A ASN* 1.3 60.6 + - - +
22A MET* 3.7 4.4 + - + -
89A ILE* 4.3 3.0 - - - +
91A GLN* 3.3 17.8 + - - -
93A THR* 4.2 6.9 - - - +
98A PHE* 3.4 28.9 - - + -
99A LEU 2.7 9.6 + - - +
100A ILE* 3.3 20.5 - - + +
101A ASN 2.7 31.7 + - - -
338A ILE* 3.4 25.0 + - + +
339A VAL* 2.9 29.2 + - + +
342A LEU* 3.0 31.9 + - + -
343A PRO 3.9 6.5 - - - +
344A SER* 3.6 4.8 - - - -
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Residues in contact with ASN 21 (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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19A VAL* 3.7 6.4 - - - +
20A ARG* 1.3 68.9 - - - +
22A MET* 1.3 58.4 + - - +
101A ASN* 3.3 25.0 - - + +
103A ILE* 5.1 1.8 - - + -
121A VAL 4.0 15.5 - - - +
122A THR* 4.0 2.5 - - - -
123A ASP* 2.6 38.0 + - - +
124A GLY 3.0 7.3 + - - -
343A PRO 4.7 4.4 + - - -
345A PRO* 3.0 29.0 - - - +
399A ARG* 3.5 22.4 - - - +
451A GLY 3.3 10.1 + - - +
453A ILE* 3.5 21.2 + - + +
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Residues in contact with MET 22 (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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20A ARG 4.3 3.1 - - - +
21A ASN* 1.3 75.5 - - - +
23A SER* 1.3 80.9 + - - +
24A VAL* 4.4 6.5 - - + -
39A LEU* 5.5 3.1 - - + -
100A ILE* 3.8 28.3 - - + -
101A ASN 3.1 8.8 + - - +
102A LEU* 3.8 16.4 - - + -
103A ILE* 3.0 24.8 + - - +
122A THR* 3.6 10.6 - - - +
124A GLY 3.3 23.6 - - - +
126A LEU* 3.7 24.9 - - + +
338A ILE* 3.9 24.9 - - + -
342A LEU* 3.8 17.3 - - + -
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Residues in contact with SER 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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22A MET* 1.3 84.0 - - - +
24A VAL* 1.3 66.1 + - - +
25A ILE* 4.0 4.0 - - - +
102A LEU* 4.5 2.0 - - - -
103A ILE* 3.9 16.2 - - - -
105A SER* 4.1 9.0 - - - -
118A ALA* 5.3 5.4 - - - -
119A LEU* 3.8 19.0 - - - +
122A THR* 3.7 20.6 + - - -
124A GLY 3.5 5.4 + - - -
125A ALA* 3.5 6.5 - - - +
126A LEU 3.0 22.9 + - - -
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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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22A MET* 4.4 2.0 - - + -
23A SER* 1.3 79.8 - - - +
25A ILE* 1.3 63.4 + - - +
26A ALA* 3.5 10.9 + - + -
32A LYS* 3.6 32.7 + - + +
35A LEU* 6.0 1.8 - - + -
36A THR* 3.6 21.3 - - + +
39A LEU* 6.2 2.2 - - + -
102A LEU* 3.6 23.9 - - + +
103A ILE 4.7 0.2 + - - -
105A SER* 3.7 11.8 + - - +
126A LEU* 3.5 30.7 - - + +
128A VAL* 4.3 17.3 - - + -
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Residues in contact with ILE 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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23A SER* 4.2 9.2 - - - +
24A VAL* 1.3 70.5 - - - +
26A ALA* 1.3 63.7 + - - +
119A LEU* 4.3 6.7 - - + -
125A ALA* 3.2 35.2 - - + -
126A LEU 3.1 6.5 + - - +
127A VAL* 3.4 18.5 - - + +
128A VAL 2.9 26.7 + - - +
139A THR* 3.9 23.6 - - + +
142A VAL* 3.7 40.6 - - + +
143A LEU* 4.4 6.1 - - + +
146A ALA* 4.2 18.4 - - + -
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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