Contacts of the strand formed by residues 191 - 200 (chain D) in PDB entry 4JZJ
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 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D GLY* 4.0 9.6 - - - -
102D LYS* 2.8 32.4 + - - +
190D PHE* 1.3 75.2 - - - +
192D ILE* 1.3 59.6 + - - +
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Residues in contact with ILE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D GLY* 4.8 1.1 - - - -
105D ALA* 3.7 7.4 - - + -
106D GLY* 3.4 33.2 - - - +
131D PRO* 3.6 37.7 - - + -
134D VAL* 3.9 13.5 - - + -
136D TYR* 4.3 0.2 - - + -
185D GLY* 3.5 34.8 + - - +
186D ARG* 3.7 24.0 - - - +
187D SER* 3.7 8.7 - - - +
190D PHE* 3.9 3.8 - - + +
191D GLY* 1.3 77.5 - - - +
193D PRO* 1.3 68.0 - - - +
194D CYS* 3.8 1.0 + - - +
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Residues in contact with PRO 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ASN* 5.0 11.4 - - - +
100D SER 3.9 18.2 - - - +
101D GLY* 3.9 2.7 - - - +
102D LYS 3.1 35.2 - - - +
103D PRO* 5.1 2.2 - - + -
104D TRP* 5.6 0.4 - - - -
105D ALA 3.2 22.9 - - - +
106D GLY* 3.5 20.5 - - - -
107D ALA 4.4 0.5 + - - -
183D VAL 4.6 0.2 - - - +
185D GLY 4.2 4.0 + - - -
192D ILE* 1.3 90.4 - - + +
194D CYS* 1.3 62.8 + - - +
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Residues in contact with CYS 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 4.1 6.1 - - - -
76D CYS* 2.1 58.1 - - - +
106D GLY 5.9 0.2 - - - -
107D ALA 5.4 0.2 - - - -
182D LEU* 4.2 6.3 - - + -
183D VAL 3.5 15.3 - - - +
184D ARG* 4.0 27.1 - - + +
185D GLY 4.9 0.4 - - - +
192D ILE 3.8 0.9 + - - +
193D PRO* 1.3 80.5 - - - +
195D THR* 1.3 63.9 + - - +
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Residues in contact with THR 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D CYS* 3.5 8.8 - - + -
77D GLU* 6.1 4.3 - - + -
107D ALA* 2.7 41.8 + - - +
109D ASN 5.5 2.0 - - - +
110D LEU* 4.4 26.2 - - + +
182D LEU* 3.5 1.2 - - - +
183D VAL* 2.8 32.7 + - - -
194D CYS* 1.3 78.0 + - - +
196D ASP* 1.3 71.6 + - - +
197D LYS* 5.3 4.5 - - + -
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Residues in contact with ASP 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D SER* 2.6 29.7 + - - -
75D LEU* 2.8 25.0 + - - +
76D CYS* 3.4 10.1 - - - +
77D GLU* 5.0 1.9 - - - +
110D LEU* 4.2 3.1 - - - -
180D HIS* 2.6 30.6 + - - +
181D ILE 3.1 18.4 - - - +
182D LEU* 3.8 8.1 - - + -
195D THR* 1.3 80.8 - - - +
197D LYS* 1.3 68.6 + - - +
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Residues in contact with LYS 197 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D ASN* 6.0 0.4 - - - +
110D LEU* 3.4 50.1 + - + +
111D THR* 5.8 0.7 - - - -
112D CYS* 5.9 3.4 - - + +
180D HIS* 3.2 8.6 - - - -
181D ILE* 3.0 33.8 + - + -
195D THR* 5.3 5.2 - - + -
196D ASP* 1.3 86.0 - - - +
198D PHE* 1.3 67.4 + - - +
199D VAL* 4.6 11.7 - - + -
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Residues in contact with PHE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLY 4.7 7.4 - - - -
72D ALA* 3.6 35.2 - - + -
178D SER* 3.2 37.5 - - - -
179D SER* 3.7 19.3 - - - -
180D HIS* 4.3 15.7 - + + +
197D LYS* 1.3 79.0 - - - +
199D VAL* 1.3 64.5 + - - +
200D VAL* 4.4 14.1 - - + -
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D CYS* 4.3 15.9 - - + +
120D LEU* 5.5 1.8 - - + -
178D SER* 3.2 4.8 - - - -
179D SER* 3.0 41.5 + - - +
181D ILE* 4.6 12.1 - - + -
197D LYS* 4.6 13.7 - - + -
198D PHE* 1.3 79.9 - - - +
200D VAL* 1.3 62.6 + - - +
201D PHE* 3.9 23.3 - - + -
204D ILE* 3.9 40.6 - - + -
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Residues in contact with VAL 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D GLN* 3.7 18.4 - - + +
178D SER* 4.2 4.0 - - - -
198D PHE* 4.4 18.6 - - + -
199D VAL* 1.3 77.6 - - - +
201D PHE* 1.3 67.3 + - - +
202D SER* 3.8 19.1 - - - +
203D GLN* 3.1 34.0 + - + +
204D ILE* 3.2 16.1 + - - +
278D TYR* 6.0 1.8 - - + +
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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