Contacts of the strand formed by residues 240 - 248 (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 HIS 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PRO* 3.8 10.3 - - + -
38B SER* 2.7 27.9 + - - +
39B SER* 3.5 29.2 - - - -
42B MET* 3.6 27.6 - - + -
100B THR* 3.9 16.9 + - - -
101B LYS* 5.2 1.0 + - - -
129B PHE* 5.8 2.0 - + + -
130B ILE 3.7 5.2 - - - +
131B TYR* 3.6 31.7 - + - -
132B PHE* 4.0 4.4 - - - -
236B ARG* 3.4 14.4 - - - +
237B PRO* 3.2 18.6 - - + +
238B GLY 3.7 0.4 - - - -
239B HIS* 1.3 95.6 + - + +
241B ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 241 (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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42B MET* 3.6 2.5 - - - -
129B PHE* 3.3 7.8 - - - -
130B ILE* 2.9 36.1 + - + +
132B PHE* 3.6 21.5 - - + -
156B LEU* 3.8 26.0 - - + +
235B LEU 3.4 6.7 - - - +
236B ARG* 4.0 11.4 - - - -
240B HIS* 1.3 76.1 - - - +
242B ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 242 (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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42B MET* 3.6 18.4 - - + -
127B MET* 4.1 14.1 - - + -
128B LYS 3.2 8.3 - - - +
129B PHE* 4.0 14.8 - - + -
156B LEU* 3.6 4.2 - - - +
234B HIS* 3.1 9.7 - - - +
235B LEU* 2.9 42.7 + - + -
241B ALA* 1.3 75.8 - - - +
243B HIS* 1.3 61.6 + - - +
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Residues in contact with HIS 243 (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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126B SER 3.4 2.1 - - - +
127B MET* 3.3 5.6 - - - -
128B LYS* 2.8 50.4 + - + +
152B HIS* 3.4 34.0 + + + +
156B LEU* 3.8 19.6 - - + +
231B THR* 3.6 33.0 + - + -
233B GLY 3.8 7.2 + - - -
234B HIS* 4.7 5.8 - + - +
242B ALA* 1.3 74.9 - - - +
244B MET* 1.3 63.4 + - - +
245B GLN* 3.0 42.7 + - + +
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Residues in contact with MET 244 (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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49B VAL* 3.7 24.0 - - + -
50B PHE* 4.5 7.2 - - + -
53B VAL* 4.1 8.3 - - + -
125B PHE* 3.9 28.3 - - + -
126B SER 3.3 15.5 - - - +
127B MET* 3.7 30.7 - - + -
174B ILE* 4.8 9.2 - - + -
231B THR* 3.9 2.6 - - - +
232B ILE* 2.9 61.2 + - + -
233B GLY 2.9 22.0 + - - +
242B ALA 4.3 0.2 - - - -
243B HIS* 1.3 74.7 - - - +
245B GLN* 1.3 67.0 + - - +
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Residues in contact with GLN 245 (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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124B VAL 4.3 0.2 - - - -
125B PHE* 3.5 4.9 - - - -
126B SER* 3.0 31.9 + - - +
128B LYS* 4.1 12.5 + - - +
152B HIS* 3.2 27.7 + - - -
229B SER* 4.6 9.6 + - - -
230B VAL 3.6 8.4 + - - +
231B THR* 4.3 7.9 + - - +
232B ILE* 4.2 7.5 - - - +
243B HIS* 3.0 39.7 + - + +
244B MET* 1.3 76.3 - - - +
246B CYS* 1.3 62.0 + - - +
247B TRP* 3.4 42.6 - - + -
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Residues in contact with CYS 246 (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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124B VAL 3.2 4.7 - - - -
125B PHE* 3.5 40.2 - - + -
181B LEU* 3.8 22.2 - - + -
186B LEU* 4.5 2.5 - - - -
229B SER* 3.1 22.3 - - - -
230B VAL* 3.1 14.3 + - + +
232B ILE* 4.0 2.9 - - + -
245B GLN* 1.3 78.0 - - - +
247B TRP* 1.3 73.2 + - - +
248B SER* 4.2 6.7 - - - -
251B MET* 3.4 14.7 - - - +
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Residues in contact with TRP 247 (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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123B GLU* 3.3 1.2 - - - +
124B VAL* 2.6 56.7 + - + +
126B SER* 3.5 27.1 - - - -
128B LYS* 4.2 16.4 - - - -
221B TYR* 4.1 6.1 - - - -
223B LEU* 3.5 33.9 - - + +
227B ILE* 3.7 31.2 - - + -
228B GLN 3.5 5.8 - - - +
229B SER* 3.4 26.4 + - - -
245B GLN* 3.4 43.1 - - + -
246B CYS* 1.3 75.2 - - - +
248B SER* 1.3 63.0 + - - +
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Residues in contact with SER 248 (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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122B ILE 3.4 6.3 - - - -
123B GLU* 2.6 32.3 + - - +
186B LEU* 3.8 21.6 - - - +
227B ILE* 3.6 14.2 - - - +
228B GLN* 3.3 13.2 + - - +
246B CYS* 4.2 2.7 - - - -
247B TRP* 1.3 76.0 - - - +
249B LYS* 1.3 60.1 + - - +
250B SER* 3.1 16.5 + - - -
251B MET* 3.5 20.9 + - - +
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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