Contacts of the strand formed by residues 183 - 189 (chain D) in PDB entry 2B5L
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 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114D VAL* 4.8 3.1 - - + -
115D LEU 3.7 10.3 - - - +
116D ASP* 4.1 7.2 - - + +
179D TRP* 3.6 1.7 - - - -
180D VAL* 2.8 60.0 + - + +
182D ASP* 1.3 76.4 - - - +
184D VAL* 1.3 62.0 + - - +
185D LYS* 3.6 30.3 + - + +
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Residues in contact with VAL 184 (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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114D VAL* 3.4 11.5 - - - +
115D LEU* 3.2 31.8 + - + +
117D LEU* 4.0 19.7 - - + -
133D ALA* 3.7 32.3 - - + +
137D LYS* 4.5 2.9 - - + -
177D ILE* 3.3 24.0 - - + -
178D GLY 3.3 12.8 - - - +
179D TRP* 4.2 17.3 - - + -
182D ASP 3.8 12.3 - - - +
183D GLU* 1.3 77.6 - - - +
185D LYS* 1.3 66.1 + - - +
186D VAL* 5.3 0.2 - - - -
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Residues in contact with LYS 185 (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 PRO* 3.8 22.4 - - + +
102D LEU* 4.1 23.6 - - + +
112D GLN* 6.2 2.0 - - + -
113D THR 3.5 2.7 - - - +
114D VAL* 3.2 44.7 - - + +
176D SER 3.6 0.5 - - - +
177D ILE* 3.2 6.8 - - - +
178D GLY 3.0 29.8 + - - +
180D VAL* 5.9 2.0 - - + -
183D GLU* 3.6 27.3 + - + +
184D VAL* 1.3 77.2 - - - +
186D VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 186 (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 PRO* 5.0 0.7 - - - -
111D THR 4.3 0.2 - - - +
112D GLN* 3.1 7.3 - - - +
113D THR* 2.6 53.4 + - - +
129D GLY* 3.7 12.1 - - - +
132D LEU* 5.5 0.4 - - + -
133D ALA* 3.7 25.4 - - + -
175D TYR* 4.0 27.8 - - + -
176D SER 3.2 8.3 - - - +
177D ILE* 3.6 28.7 - - + -
185D LYS* 1.3 80.6 - - - +
187D THR* 1.3 67.1 + - - +
188D GLU* 4.5 1.3 - - - +
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Residues in contact with THR 187 (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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98D ILE* 4.7 13.5 - - + -
101D PRO* 4.2 18.3 + - - +
106D ASP* 5.7 2.0 - - + +
107D SER* 5.8 1.3 - - - +
110D SER* 4.1 12.3 - - - -
111D THR 3.8 0.4 - - - -
112D GLN* 2.6 33.7 + - - +
174D GLU 3.3 1.0 - - - +
175D TYR* 3.2 5.5 - - - -
176D SER* 3.0 39.7 + - - -
186D VAL* 1.3 76.2 + - - +
188D GLU* 1.3 64.5 + - - +
189D TRP* 3.5 14.6 - - + -
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Residues in contact with GLU 188 (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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110D SER* 3.0 28.2 - - - -
111D THR* 1.7 64.2 + - - +
112D GLN* 3.2 3.3 + - - -
113D THR* 3.3 18.4 + - - -
126D SER* 3.4 17.4 + - - +
129D GLY* 4.2 1.6 - - - -
173D ARG* 3.3 20.4 - - - +
174D GLU 2.9 11.0 - - - +
175D TYR* 3.7 26.9 - - + -
186D VAL* 4.5 1.2 - - - +
187D THR* 1.3 76.9 - - - +
189D TRP* 1.3 66.9 + - - +
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Residues in contact with TRP 189 (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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98D ILE* 3.3 41.0 - - + +
109D PRO 2.9 26.7 - - - +
110D SER* 4.4 1.6 - - - -
143D ARG* 4.1 8.3 - - - -
172D ARG 3.6 0.7 - - - +
173D ARG* 3.5 17.5 - - - +
174D GLU* 2.9 80.3 + - + +
175D TYR 4.0 6.5 - - - -
176D SER* 4.2 4.7 - - - -
187D THR* 3.5 19.3 - - + -
188D GLU* 1.3 80.0 - - - +
190D CYS* 1.0 83.6 + - - +
191D ASN* 3.4 18.5 + - - -
201D ALA* 4.1 13.7 - - + -
202D ARG 4.0 11.7 - - - -
203D ARG* 3.8 20.3 - - + +
221D ASP* 3.8 0.2 - - - -
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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