Contacts of the strand formed by residues 97 - 104 (chain B) in PDB entry 2B4M
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 GLU 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B SER 2.8 5.6 + - - -
96B ALA* 1.3 75.7 - - - +
98B GLU* 1.3 65.8 + - - +
225B TRP* 3.5 7.4 - - + +
226B LEU 3.4 9.2 - - - +
227B PRO* 3.0 8.1 - - - +
228B ASN* 2.6 36.4 + - - +
229B THR* 2.3 42.9 + - - +
250B GLY* 3.5 6.6 + - - +
251B VAL* 3.4 58.3 + - + +
253B MET* 3.5 20.6 - - + -
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Residues in contact with GLU 98 (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* 3.7 12.2 - - - +
97B GLU* 1.3 81.3 - - - +
99B ILE* 1.3 64.1 + - - +
100B HIS* 2.8 32.0 + - + +
225B TRP* 3.4 5.4 - - - +
226B LEU 2.7 33.9 + - - +
227B PRO* 6.2 0.2 - - - -
246B THR* 3.4 16.1 + - + +
248B MET 3.2 13.0 - - - +
249B THR* 4.0 18.4 - - - +
251B VAL* 4.1 3.1 - - - -
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Residues in contact with ILE 99 (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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74B PRO* 4.7 2.9 - - + -
98B GLU* 1.3 74.8 - - - +
100B HIS* 1.3 58.5 + - - +
128B MET* 4.2 19.5 - - + -
181B GLU* 3.9 12.8 - - - +
184B SER* 5.9 1.6 - - - +
222B LEU 3.6 21.8 - - - +
224B ALA 3.4 8.3 - - - +
225B TRP* 3.6 36.8 - - + +
246B THR* 3.5 4.5 - - - +
247B SER* 2.7 46.5 + - - +
248B MET* 2.8 36.5 + - + +
251B VAL* 4.0 11.7 - - + -
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Residues in contact with HIS 100 (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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98B GLU* 2.8 41.2 + - + +
99B ILE* 1.3 80.5 - - - +
101B THR* 1.3 62.6 + - - +
102B ILE* 3.9 2.1 + - + -
222B LEU* 3.8 13.0 - - - -
224B ALA* 2.7 42.3 + - + +
226B LEU* 3.8 21.9 + - + +
243B ASP* 2.5 35.2 + - - +
245B GLY 3.4 4.0 - - - +
246B THR* 3.2 18.9 + - - -
247B SER* 4.4 1.6 - - - -
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Residues in contact with THR 101 (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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100B HIS* 1.3 71.7 - - - +
102B ILE* 1.3 63.9 + - - +
118B LEU* 3.5 44.2 + - + +
121B PHE* 4.2 2.4 + - - -
220B ALA* 5.7 0.4 - - + -
221B SER 3.7 5.4 - - - +
222B LEU* 3.7 27.6 - - + +
243B ASP* 3.8 0.7 - - - +
244B ILE* 3.0 33.3 + - + +
245B GLY* 2.7 23.4 + - - +
247B SER* 4.1 15.2 + - - -
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Residues in contact with ILE 102 (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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100B HIS* 3.9 1.5 + - + -
101B THR* 1.3 79.1 - - - +
103B THR* 1.3 64.3 + - - +
209B MET* 4.6 6.7 - - - -
210B TRP* 3.8 36.3 - - + -
213B ILE* 4.0 28.8 - - + +
220B ALA* 3.4 2.9 - - - +
221B SER* 2.9 47.8 + - - +
224B ALA* 3.9 23.3 - - + -
226B LEU* 5.0 0.7 - - + -
241B TYR* 3.9 20.4 - - + -
242B ASP 3.1 12.6 - - - +
243B ASP* 4.1 11.4 - - - +
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Residues in contact with THR 103 (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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101B THR* 4.5 0.6 + - + -
102B ILE* 1.3 77.9 - - - +
104B ARG* 1.3 62.6 + - - +
107B PHE* 3.7 29.8 - - + +
108B SER* 4.9 1.6 + - - -
118B LEU* 3.9 3.1 - - + -
213B ILE* 3.2 17.2 - - - +
219B ASP 3.3 8.7 - - - -
220B ALA* 3.8 15.5 - - + +
241B TYR* 3.5 0.7 - - - +
242B ASP* 2.8 48.7 + - - +
244B ILE* 3.6 30.0 - - + +
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Residues in contact with ARG 104 (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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103B THR* 1.3 78.6 - - - +
105B LYS* 1.3 77.1 + - - +
106B GLY 3.1 1.1 + - - -
107B PHE* 3.0 36.8 + - + +
110B GLU* 1.8 52.2 + - - +
111B GLN* 5.1 3.6 + - - -
213B ILE* 3.3 25.6 - - - +
216B GLY* 3.6 25.4 + - - -
218B ALA 3.5 21.8 - - - +
219B ASP* 3.1 27.7 + - - +
242B ASP* 3.6 4.1 - - - +
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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