Contacts of the strand formed by residues 190 - 197 (chain B) in PDB entry 4TTB
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 ILE 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B GLN* 3.4 20.9 - - - +
111B VAL* 3.5 26.7 - - + +
113B MET* 5.9 1.6 - - - -
116B ILE* 4.9 9.9 - - + -
139B VAL* 4.0 13.0 - - + -
140B VAL 3.6 2.2 - - - -
141B LYS* 3.7 31.6 - - + -
188B ALA* 3.2 3.2 - - - +
189B PRO* 1.3 95.5 - - + +
191B LEU* 1.3 75.4 - - - +
192B ILE* 3.9 18.4 - - + -
264B PRO* 3.7 2.1 - - - +
265B VAL* 2.9 42.9 + - + +
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Residues in contact with LEU 191 (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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138B VAL 3.4 1.6 - - - +
139B VAL* 3.3 3.8 - - - -
140B VAL* 2.8 42.5 + - + +
146B LYS* 3.9 23.3 - - + +
149B ILE* 3.8 33.9 - - + -
185B LEU* 3.9 32.5 - - + +
188B ALA* 4.8 2.2 - - + -
190B ILE* 1.3 77.1 - - - +
192B ILE* 1.3 61.9 + - - +
193B LEU* 3.9 15.1 + - + +
262B LEU* 4.0 12.3 - - + -
263B LEU 3.7 0.9 - - - -
264B PRO* 3.6 31.0 - - + -
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 4.8 7.9 - - + -
119B VAL* 5.0 4.9 - - + -
120B ILE* 4.3 16.8 - - + -
137B PHE* 4.5 13.5 - - + -
138B VAL 3.4 5.4 - - - +
139B VAL* 4.3 9.9 - - + -
190B ILE* 3.9 16.8 - - + -
191B LEU* 1.3 76.3 - - - +
193B LEU* 1.3 64.1 + - - +
194B ILE* 3.9 24.6 - - + +
224B LEU* 4.5 23.1 - - + -
228B LEU* 5.2 1.3 - - + -
261B MET 3.8 0.7 - - - +
262B LEU* 3.4 2.9 - - - -
263B LEU* 2.8 46.8 + - + +
265B VAL* 4.0 20.9 - - + -
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Residues in contact with LEU 193 (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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136B THR 3.4 2.8 - - - +
138B VAL* 2.7 41.9 + - + +
140B VAL* 4.0 17.5 - - + -
149B ILE* 4.4 11.4 - - + -
191B LEU* 3.9 23.3 - - + +
192B ILE* 1.3 76.3 - - - +
194B ILE* 1.3 62.5 + - - +
195B PHE* 3.5 18.9 - - + -
247B LEU* 4.7 11.4 - - + -
251B LEU* 3.7 20.2 - - + -
259B LEU* 4.0 18.8 - - + -
261B MET 3.5 3.1 - - - -
262B LEU* 3.9 31.4 - - + -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TRP* 4.9 0.9 - - + -
136B THR 3.4 6.3 - - - +
137B PHE* 3.4 37.7 - - + -
192B ILE* 3.9 21.3 - - + +
193B LEU* 1.3 72.2 - - - +
195B PHE* 1.3 64.0 + - - +
217B VAL* 3.5 29.8 - - + -
221B CYS* 3.8 16.2 - - - -
224B LEU* 3.9 13.5 - - + -
259B LEU* 3.3 2.6 - - - +
260B LEU* 3.0 28.4 + - + +
261B MET* 3.0 32.2 + - + +
263B LEU* 4.2 8.3 - - + -
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Residues in contact with PHE 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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135B TRP* 3.3 9.5 - - - +
136B THR* 2.8 35.9 + - - +
138B VAL* 3.4 28.9 - - + -
193B LEU* 3.5 26.5 - - + -
194B ILE* 1.3 76.8 - - - +
196B LYS* 1.3 59.5 - - - +
197B GLN 3.8 0.2 + - - -
217B VAL* 4.2 2.3 - - - +
247B LEU 5.0 0.9 - - - -
248B ARG* 4.1 27.6 - - + -
251B LEU* 4.4 12.8 - - + -
253B ARG* 4.1 14.1 - - + -
257B GLU* 3.7 36.3 - - + +
258B LYS 3.4 5.8 - - - +
259B LEU* 3.6 37.7 - - + -
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Residues in contact with LYS 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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134B PRO 3.6 4.3 - - - -
194B ILE 4.3 0.6 + - - -
195B PHE* 1.3 72.3 - - - +
197B GLN* 1.3 62.3 + - - +
198B VAL* 3.6 24.5 + - + +
213B ASN* 3.7 20.5 - - + +
214B GLU* 3.5 48.5 + - + +
217B VAL* 4.0 16.0 - - + +
256B HIS 3.5 0.3 - - - +
257B GLU* 3.2 3.3 - - - -
258B LYS* 2.8 49.2 + - - +
260B LEU* 4.6 16.9 - - + +
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Residues in contact with GLN 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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280A LYS* 4.3 14.3 + - - +
284A GLN 5.1 4.2 + - - -
132B THR 5.0 1.0 - - - +
133B GLU 4.6 1.8 + - - -
134B PRO* 3.0 32.9 + - + +
135B TRP 3.1 16.2 + - - +
136B THR* 2.7 29.1 + - - +
196B LYS* 1.3 72.4 - - - +
198B VAL* 1.3 62.5 + - - +
213B ASN* 3.5 23.7 + - - -
256B HIS* 3.4 17.0 - - + +
257B GLU* 3.9 15.1 + - + +
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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