Contacts of the strand formed by residues 193 - 201 (chain B) in PDB entry 4TZM
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 PHE 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B ASN 5.0 0.7 - - - -
59B ILE* 4.1 34.3 - - + -
112B VAL* 4.0 18.8 - - + -
113B THR 3.2 13.7 - - - +
114B GLU 3.9 8.3 + - - -
122B ILE* 4.8 6.5 - - + -
189B LEU* 4.2 20.2 - - + -
190B PRO* 3.6 20.4 - - + -
192B GLU* 1.3 74.9 - - - +
194B THR* 1.3 73.9 + - - +
195B ALA* 4.0 5.8 - - + -
496D ILE* 4.4 6.7 - - + -
497D ASN* 3.3 4.2 - - - +
498D ARG* 2.9 80.3 + - + +
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Residues in contact with THR 194 (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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111B VAL 3.7 0.9 - - - +
112B VAL* 3.4 0.2 - - - -
113B THR* 2.5 55.6 + - - +
114B GLU 4.2 0.9 + - - -
115B HIS 4.3 0.8 - - - -
116B ASP* 3.3 42.5 + - + +
117B GLY* 5.3 0.9 - - - -
193B PHE* 1.3 78.0 + - - +
195B ALA* 1.3 66.0 + - - +
196B ASN* 4.1 5.0 + - + +
198B ARG* 5.9 0.9 - - - +
495D SER* 4.1 16.4 - - - +
496D ILE 3.2 7.4 - - - +
497D ASN* 3.3 14.6 - - - +
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Residues in contact with ALA 195 (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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59B ILE* 3.8 28.7 - - + -
110B LEU* 4.2 14.4 - - + -
111B VAL 3.2 6.3 - - - +
112B VAL* 4.2 9.6 - - + +
193B PHE* 4.0 6.7 - - + -
194B THR* 1.3 74.8 - - - +
196B ASN* 1.3 59.9 + - - +
495D SER* 3.5 6.4 - - - -
496D ILE* 2.6 43.1 + - + +
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Residues in contact with ASN 196 (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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110B LEU* 3.4 6.5 - - - +
111B VAL* 2.5 45.7 + - - +
116B ASP* 5.3 3.8 - - - +
117B GLY* 5.7 2.4 - - - -
194B THR* 5.3 4.6 - - + +
195B ALA* 1.3 72.4 - - - +
197B PHE* 1.3 61.2 + - - +
198B ARG* 3.4 33.5 + - - +
491D VAL* 3.3 23.1 - - - +
492D SER* 2.7 35.6 + - - +
494D THR 4.1 0.2 + - - -
495D SER* 3.6 23.5 - - - +
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Residues in contact with PHE 197 (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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50B PHE* 3.7 26.7 - + + -
54B LEU* 4.2 21.1 - - + -
89B ILE* 3.9 22.2 - - + -
92B LEU* 4.7 15.7 - - + -
93B LEU* 3.7 31.2 - - + -
108B ILE* 4.3 9.4 - - + -
109B SER 3.3 13.9 - - - -
110B LEU* 3.9 21.3 - - + -
195B ALA 6.2 0.2 - - - -
196B ASN* 1.3 77.9 + - - +
198B ARG* 1.3 64.6 + - - +
214B PHE* 3.6 21.5 - + + -
492D SER* 2.9 35.4 + - - +
494D THR 6.0 0.4 - - - -
496D ILE* 5.7 4.3 - - + -
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Residues in contact with ARG 198 (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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108B ILE* 3.7 1.0 - - - +
109B SER* 2.9 31.2 + - - +
111B VAL* 3.6 31.3 - - + +
113B THR* 3.7 18.4 + - - +
117B GLY* 4.6 4.4 - - - -
118B ASP 3.0 32.3 + - - +
119B VAL* 4.0 11.1 + - - +
194B THR* 5.9 1.2 - - - +
196B ASN* 3.4 34.0 + - + +
197B PHE* 1.3 80.1 - - - +
199B LEU* 1.3 63.0 + - - +
214B PHE* 4.6 0.9 - - - -
220B PHE* 3.2 46.9 + - + -
221B TYR* 4.1 1.0 - - - +
490D GLY 3.2 8.7 - - - +
491D VAL* 3.9 19.4 - - + +
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Residues in contact with LEU 199 (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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96B ALA* 4.4 7.6 - - + -
105B LEU* 3.8 13.2 - - + -
107B GLU 3.1 13.9 - - - +
108B ILE* 4.2 5.4 - - + -
198B ARG* 1.3 75.4 - - - +
200B LYS* 1.3 60.5 + - - +
201B TYR* 3.6 35.9 - - + +
211B ILE* 3.7 22.7 - - + -
214B PHE* 3.5 45.5 - - + -
220B PHE* 3.5 11.0 - - - -
489D TYR* 3.3 4.2 - - - -
490D GLY* 2.7 42.1 + - - -
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Residues in contact with LYS 200 (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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105B LEU* 3.9 4.0 - - - +
106B LYS* 2.8 49.2 + - + +
107B GLU* 2.9 18.3 + - + +
199B LEU* 1.3 77.1 - - - +
201B TYR* 1.3 73.5 + - - +
220B PHE* 4.0 15.9 - - + -
487D ALA* 5.0 11.6 - - - +
488D ARG 3.7 6.3 - - - +
489D TYR* 3.8 35.1 + - + -
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Residues in contact with TYR 201 (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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104B PHE 3.4 13.7 - - - -
106B LYS* 4.0 2.9 - - - +
199B LEU* 3.6 23.3 - - + +
200B LYS* 1.3 90.3 - - - +
202B THR* 1.3 71.4 + - - +
205B ALA* 4.0 13.0 - - + -
209B PHE* 4.0 14.4 - + - -
210B ARG* 3.7 11.3 - - - +
211B ILE* 3.1 48.3 + - + +
214B PHE* 4.7 4.5 + - - +
216B ASP* 4.4 2.3 + - - -
487D ALA* 5.4 3.5 - - - +
488D ARG* 3.2 73.2 + - + +
489D TYR 4.1 11.4 - - - -
490D GLY* 4.2 1.5 - - - -
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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