Contacts of the helix formed by residues 202 - 210 (chain A) in PDB entry 4Z1H
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 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN* 3.9 5.9 + - - -
201A PHE* 1.3 75.4 + - - -
203A VAL* 1.3 66.5 + - - +
204A GLY* 3.0 4.9 + - - -
205A PHE* 3.2 6.2 + - - +
601A 4KP 3.1 64.0 - - - +
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Residues in contact with VAL 203 (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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97A LEU* 4.2 22.4 - - + -
101A VAL* 4.0 26.4 - - + +
105A LEU* 5.6 3.1 - - + -
106A TYR* 5.5 0.2 - - - -
201A PHE* 3.7 15.8 - - + +
202A GLY* 1.3 80.6 - - - +
204A GLY* 1.3 63.9 + - - +
205A PHE 2.9 1.9 + - - -
206A TYR* 2.9 28.8 + - + +
207A SER 4.2 0.7 + - - -
601A 4KP 4.2 3.5 - - + +
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Residues in contact with GLY 204 (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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101A VAL* 5.8 0.7 - - - -
106A TYR* 4.3 12.7 + - - -
115A GLU* 3.9 29.8 - - - +
116A LEU* 4.9 0.3 - - - +
119A ASN* 4.3 4.9 - - - -
201A PHE 4.6 4.6 - - - +
202A GLY 3.0 3.0 + - - -
203A VAL* 1.3 76.8 - - - +
205A PHE* 1.3 56.3 + - - +
207A SER* 2.4 34.7 + - - -
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Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.0 13.7 - - + +
119A ASN* 3.6 6.2 - - - +
202A GLY 3.2 4.4 + - - +
203A VAL 2.9 0.6 + - - -
204A GLY* 1.3 75.9 - - - +
206A TYR* 1.3 79.1 + + + +
207A SER* 4.0 0.3 + - - -
208A ALA* 2.9 32.9 + - + +
209A PHE* 4.3 5.8 - + - -
215A VAL* 4.0 11.7 - - + -
217A VAL* 4.0 8.3 - - + -
231A TRP* 3.9 26.9 - + - -
253A ILE* 3.8 34.1 - - + -
601A 4KP 3.4 74.3 - + + -
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Residues in contact with TYR 206 (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 PHE* 4.1 26.2 - + - -
94A THR* 4.1 14.5 + - - -
97A LEU* 4.6 15.3 - - + -
98A LEU* 3.5 32.3 - - + +
101A VAL* 3.7 17.7 - - + +
102A ALA* 4.8 2.4 - - - -
171A ASN 2.4 30.0 + - - -
203A VAL* 2.9 34.0 + - + +
205A PHE* 1.3 89.5 - + - +
207A SER* 1.3 61.3 + - - +
208A ALA 2.9 5.8 - - - -
209A PHE* 2.9 34.3 + + - +
210A MET 4.4 0.9 + - - -
231A TRP* 5.1 2.7 - + - -
601A 4KP 3.9 17.1 + + + -
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Residues in contact with SER 207 (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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101A VAL* 3.5 12.7 - - - +
106A TYR* 3.9 28.9 - - - -
112A PHE* 3.5 34.2 + - - +
115A GLU* 4.0 6.1 - - - +
116A LEU* 5.1 1.2 - - - +
204A GLY 2.4 23.5 + - - -
205A PHE 4.0 0.5 + - - -
206A TYR* 1.3 77.1 - - - +
208A ALA* 1.3 64.5 + - - +
210A MET* 2.9 27.3 + - - +
211A VAL 4.3 0.5 + - - -
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Residues in contact with ALA 208 (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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112A PHE* 4.3 10.8 - - - -
116A LEU* 4.9 7.4 - - + +
205A PHE* 2.9 24.5 + - + +
206A TYR 4.5 0.2 - - - -
207A SER* 1.3 81.1 + - - +
209A PHE* 1.3 58.9 + - + +
210A MET 3.2 0.7 + - - -
211A VAL* 3.4 8.9 - - - +
212A ALA* 3.1 27.8 + - - +
215A VAL* 4.3 12.1 - - + -
253A ILE* 5.6 0.4 - - + -
255A ILE* 4.2 24.6 - - + +
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Residues in contact with PHE 209 (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 PHE* 5.8 0.9 - + - -
98A LEU* 3.4 20.4 - - + -
102A ALA* 4.2 19.9 - - + +
205A PHE* 4.3 7.9 - + - -
206A TYR* 2.9 50.9 + + - +
208A ALA* 1.3 74.5 - - + +
210A MET* 1.3 55.0 + - - +
211A VAL 3.1 2.0 - - - -
212A ALA* 3.7 11.0 - - + +
214A ARG 5.5 0.9 - - - -
215A VAL* 3.6 30.5 - - + -
231A TRP* 4.1 9.9 - + - -
233A SER* 4.1 23.3 - - - -
234A ASP 4.4 1.8 - - - -
235A GLY* 3.7 33.2 - - - -
258A LYS* 2.7 25.7 + - - -
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Residues in contact with MET 210 (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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101A VAL 3.3 28.0 - - - +
102A ALA* 3.5 20.4 - - - +
103A ARG* 5.5 1.3 - - - -
104A SER 5.8 0.2 - - - -
105A LEU 5.7 0.4 - - - -
106A TYR* 4.0 34.1 - - + +
108A GLU 3.6 16.8 - - - +
109A LYS* 3.6 36.7 - - + +
111A VAL* 4.4 3.8 - - + -
112A PHE 5.1 0.7 - - - +
207A SER* 2.9 21.4 + - - +
209A PHE* 1.3 78.7 - - - +
211A VAL* 1.3 62.5 + - + +
258A LYS* 3.1 11.9 + - - +
261A CYS* 4.1 5.7 - - - -
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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