Contacts of the strand formed by residues 95 - 100 (chain B) in PDB entry 1ZJA
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 ARG 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TRP* 3.4 71.9 - - + +
47B ASP* 3.1 12.9 + - - +
48B ALA* 3.2 12.3 - - + +
49B ILE* 3.0 26.7 + - - +
89B LEU* 4.7 4.6 - - - +
93B GLY 5.0 7.5 + - - +
94B MET* 1.3 80.4 - - - +
96B LEU* 1.3 61.3 + - - +
195B SER* 3.6 22.4 + - - +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 5.8 0.7 - - - -
34B LEU* 5.7 1.1 - - + -
49B ILE* 3.5 19.7 - - + +
51B ILE* 4.1 24.0 - - + -
82B PHE* 3.8 25.6 - - + -
85B LEU* 4.5 7.6 - - + -
86B MET* 3.4 34.6 - - + +
89B LEU* 3.7 24.2 - - + +
95B ARG* 1.3 75.5 - - - +
97B MET* 1.3 67.9 + - - +
98B VAL* 3.9 11.7 - - + -
194B VAL* 3.8 4.2 - - + +
195B SER* 2.9 31.5 + - - +
196B GLY 3.2 3.2 + - - -
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.8 24.7 - - + -
49B ILE 2.8 12.2 + - - +
50B TRP* 3.2 24.6 - - + -
51B ILE* 3.0 29.6 + - - +
96B LEU* 1.3 73.7 - - - +
98B VAL* 1.3 68.5 + - - +
196B GLY* 3.2 17.0 - - - +
197B MET 3.8 7.9 - - - +
198B ARG* 3.9 18.6 - - - +
250B VAL* 3.8 24.9 - - + +
252B ALA* 4.2 9.6 - - + -
276B MET* 3.9 18.4 - - + -
278B PHE* 5.0 0.2 - - - -
362B PHE* 4.1 11.4 - - - -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TRP* 4.3 2.7 - - - -
51B ILE* 4.1 9.4 - - + -
54B HIS* 3.9 20.4 - - + +
55B TYR* 3.7 18.4 - - - +
82B PHE* 4.5 1.6 - - + -
96B LEU* 3.9 23.3 - - + -
97B MET* 1.3 78.5 - - - +
99B ASP* 1.3 60.8 + - - +
100B VAL* 4.5 1.1 - - + -
189B TRP* 5.2 4.3 - - + -
194B VAL* 3.8 30.3 - - + -
196B GLY 3.0 5.5 + - - +
197B MET* 3.3 20.1 - - + -
198B ARG 2.9 23.9 + - - -
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TRP* 3.3 24.2 + - - +
51B ILE* 3.5 8.8 + - - +
52B ASN* 3.6 1.3 + - - -
53B PRO* 3.4 31.3 - - + +
54B HIS* 5.3 0.6 + - - -
55B TYR* 2.6 36.8 + - - -
64B TYR* 2.6 32.2 + - - -
98B VAL* 1.3 74.7 - - - +
100B VAL* 1.3 64.6 + - - +
101B VAL* 4.1 1.5 - - - +
198B ARG* 2.9 27.8 + - - +
200B ASP* 3.8 4.7 - - - +
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Residues in contact with VAL 100 (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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55B TYR* 4.6 4.0 - - - +
98B VAL* 4.3 3.8 - - + +
99B ASP* 1.3 77.0 + - - +
101B VAL* 1.3 62.8 + - - +
102B ILE* 3.7 30.0 + - + -
185B MET* 4.4 4.7 - - + -
186B LEU* 3.6 24.0 - - + -
197B MET* 3.7 46.9 - - + -
198B ARG 2.8 12.6 + - - +
199B PHE* 3.6 12.7 - - + +
200B ASP 2.9 27.0 + - - +
205B TYR* 4.8 0.3 + - - -
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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