Contacts of the strand formed by residues 193 - 198 (chain A) in PDB entry 4NTX
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 GLY 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A TYR* 3.5 29.2 - - - -
189A PHE* 3.2 13.3 - - - -
190A THR 2.9 37.2 + - - -
191A ARG 3.2 1.6 + - - -
192A TYR* 1.3 79.5 - - - +
194A LYS* 1.3 61.7 + - - -
195A CYS* 3.4 3.4 + - - -
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Residues in contact with LYS 194 (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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94A CYS* 5.1 2.6 - - - -
95A ASN* 5.2 2.9 + - - +
98A GLU 5.5 1.2 + - - -
100A ARG* 5.8 1.6 - - - +
159A TYR* 3.8 21.7 - - - +
160A ASP* 2.8 45.3 + - - +
163A GLY* 4.4 14.6 + - - +
164A HIS* 4.0 12.6 + - - +
165A ASP* 5.4 6.7 + - - +
169A MET* 5.9 0.2 - - - +
187A VAL* 4.2 26.0 - - + -
188A VAL 4.4 0.2 - - - -
189A PHE* 4.0 16.8 - - + -
192A TYR 4.0 2.2 + - - -
193A GLY* 1.3 67.5 - - - -
195A CYS* 1.3 64.2 + - - +
196A TYR* 3.5 34.2 + - + +
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Residues in contact with CYS 195 (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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92A THR* 4.5 2.0 - - + -
93A PHE 3.2 6.1 - - - +
94A CYS* 2.0 50.9 - - - +
187A VAL* 3.5 6.2 - - - +
188A VAL* 2.9 45.5 + - + +
190A THR* 3.2 18.4 - - + -
192A TYR* 4.0 5.4 - - - -
193A GLY 3.7 5.6 - - - -
194A LYS* 1.3 79.4 - - - +
196A TYR* 1.3 73.3 + - - +
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Residues in contact with TYR 196 (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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91A VAL 3.5 1.9 - - - +
92A THR* 3.2 2.9 - - - -
93A PHE* 2.9 58.5 + + + -
94A CYS* 6.1 0.2 - - - -
164A HIS 2.7 29.9 + - - -
165A ASP* 3.4 3.8 + - - -
166A ILE* 3.1 49.6 + - + +
169A MET* 3.8 16.8 - - + -
185A PHE* 3.9 17.5 - - + -
186A LYS 3.5 2.0 - - - -
187A VAL* 3.7 28.5 - - + -
194A LYS* 3.5 31.8 + - + -
195A CYS* 1.3 83.7 - - - +
197A THR* 1.3 63.5 + - - +
198A PHE 4.1 0.4 - - - -
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Residues in contact with THR 197 (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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90A ALA* 3.9 14.6 - - + -
91A VAL 3.3 4.5 - - - +
92A THR* 2.9 25.0 + - - +
184A ASP 3.8 1.0 - - - +
185A PHE* 3.4 4.5 - - - -
186A LYS* 2.8 42.4 + - - +
188A VAL* 3.3 20.7 - - - +
196A TYR* 1.3 73.9 - - - +
198A PHE* 1.3 72.6 + - - +
199A ASN 3.8 0.3 + - - -
200A ALA* 3.8 23.6 + - + -
202A GLN* 6.0 1.1 - - - +
251A HIS* 4.5 3.7 - - + +
257A PRO* 5.2 1.6 - - - +
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Residues in contact with PHE 198 (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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88A PHE* 4.3 11.0 - + - -
90A ALA* 3.5 0.9 - - - -
91A VAL* 2.6 46.0 + - + +
175A PHE* 3.9 26.2 - + + -
180A CYS* 4.0 21.8 - - + -
184A ASP* 3.9 22.2 - - + -
185A PHE* 3.7 34.2 - + + -
197A THR* 1.3 73.3 - - - +
199A ASN* 1.3 78.7 + - + +
200A ALA 3.3 0.7 + - - -
208A LEU* 3.5 32.8 - - + -
219A LEU* 3.9 28.0 - - + -
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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