Contacts of the strand formed by residues 95 - 100 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TRP* 3.2 68.6 - - + +
47A ASP* 3.1 20.0 + - - +
48A ALA* 3.2 14.3 - - + +
49A ILE* 3.0 26.5 + - - +
89A LEU* 4.6 5.0 - - - +
93A GLY 4.9 8.0 + - - +
94A MET* 1.3 80.3 - - - +
96A LEU* 1.3 60.6 + - - +
195A SER* 3.5 24.0 - - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 5.9 0.4 - - - -
34A LEU* 5.9 0.7 - - + -
49A ILE* 3.6 14.4 - - + +
51A ILE* 4.0 24.5 - - + -
82A PHE* 3.8 24.7 - - + -
85A LEU* 4.6 7.4 - - + -
86A MET* 3.3 33.4 - - + -
89A LEU* 3.6 24.8 - - + +
95A ARG* 1.3 75.3 - - - +
97A MET* 1.3 73.6 + - - +
98A VAL* 3.9 10.5 - - + -
194A VAL* 3.9 4.3 - - + +
195A SER* 3.0 30.0 + - - +
196A GLY 3.2 3.7 + - - -
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Residues in contact with MET 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.8 19.3 - - + -
49A ILE 2.8 13.6 + - - +
50A TRP* 3.2 24.9 - - + -
51A ILE* 3.0 30.1 + - - +
96A LEU* 1.3 73.2 - - - +
98A VAL* 1.3 69.4 + - - +
196A GLY* 3.3 14.4 - - - +
197A MET 4.2 6.7 - - - +
198A ARG* 3.9 18.8 - - - +
250A VAL* 3.8 30.1 - - + +
252A ALA* 4.4 9.6 - - + -
276A MET* 4.0 15.9 - - + -
278A PHE* 5.0 0.4 - - - -
362A PHE* 4.1 13.5 - - - -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TRP* 4.3 2.5 - - - -
51A ILE* 4.1 8.3 - - + -
54A HIS* 3.7 23.1 - - + +
55A TYR* 3.8 17.5 - - - +
82A PHE* 4.4 1.8 - - + -
96A LEU* 3.9 24.9 - - + -
97A MET* 1.3 79.3 - - - +
99A ASP* 1.3 59.4 + - - +
100A VAL* 4.6 1.3 - - + -
189A TRP* 5.1 3.8 - - + -
194A VAL* 3.6 31.6 - - + -
196A GLY 3.0 5.5 + - - +
197A MET* 3.3 22.5 - - + -
198A ARG 2.9 24.1 + - - -
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Residues in contact with ASP 99 (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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50A TRP* 3.2 23.7 + - - +
51A ILE 3.5 7.6 + - - +
52A ASN* 3.6 1.3 + - - -
53A PRO* 3.5 30.5 - - + +
54A HIS* 5.2 0.6 + - - -
55A TYR* 2.6 36.0 + - - -
64A TYR* 2.6 33.7 + - - -
98A VAL* 1.3 73.7 - - - +
100A VAL* 1.3 65.4 + - - +
101A VAL* 3.8 2.2 + - - +
198A ARG* 2.9 28.4 + - - +
200A ASP* 3.8 4.2 - - - +
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Residues in contact with VAL 100 (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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55A TYR* 4.5 6.5 - - - +
98A VAL* 4.3 1.1 - - + +
99A ASP* 1.3 76.1 + - - +
101A VAL* 1.3 64.3 - - - +
102A ILE* 3.8 22.2 + - + -
185A MET* 4.5 3.8 - - + -
186A LEU* 3.7 15.7 - - + -
197A MET* 3.7 48.7 - - + -
198A ARG 2.8 13.5 + - - +
199A PHE* 3.6 27.1 - - + -
200A ASP* 2.9 28.1 + - - +
205A TYR* 4.7 0.5 + - - -
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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