Contacts of the strand formed by residues 164 - 170 (chain B) in PDB entry 4L0D
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 ARG 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A LEU* 5.5 6.1 - - - +
139B GLY 5.6 1.7 - - - +
140B ASP 3.6 6.1 + - - +
141B THR* 3.2 34.9 + - + +
142B ILE* 2.9 29.8 + - - +
162B GLY 3.8 1.2 + - - -
163B TYR* 1.3 74.1 - - - +
165B CYS* 1.3 61.9 + - - +
166B ILE* 3.8 16.8 - - - +
187B GLU* 3.2 36.4 + - - +
214B ILE* 4.3 18.4 - - - +
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Residues in contact with CYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ILE* 3.8 11.9 - - - -
154B LEU* 4.0 11.0 - - - -
155B ALA* 3.7 28.3 - - - +
158B ALA* 3.9 16.4 - - + -
163B TYR 3.8 1.4 + - - -
164B ARG* 1.3 75.9 - - - +
166B ILE* 1.3 65.6 + - - +
167B ILE* 3.5 29.2 - - - -
185B GLY 4.6 5.5 + - - +
186B ALA* 3.7 9.2 - - + -
187B GLU* 3.0 28.9 + - - +
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR* 3.8 22.2 - - + -
142B ILE 2.9 17.4 + - - +
143B ILE* 3.3 11.1 - - + +
144B GLU 2.9 26.5 + - - -
164B ARG* 3.8 21.3 - - - +
165B CYS* 1.3 80.2 - - - +
167B ILE* 1.3 72.4 + - - +
187B GLU* 3.6 24.9 - - + +
189B VAL* 4.7 7.0 - - + -
210B LEU* 4.3 22.4 - - + -
214B ILE* 4.1 18.4 - - + -
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLU* 3.6 11.7 - - + +
146B THR* 3.6 23.6 - - + -
151B GLY* 3.7 22.9 - - - +
154B LEU* 4.9 1.1 - - + -
165B CYS* 3.5 25.1 - - - -
166B ILE* 1.3 77.0 - - - +
168B VAL* 1.3 73.5 + - - +
169B MET* 4.5 7.0 - - + +
181B LEU* 4.0 36.3 - - + -
186B ALA* 4.0 9.6 - - + -
187B GLU 2.9 16.0 + - - +
188B ILE* 3.7 4.2 - - + -
189B VAL* 2.9 27.1 + - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 4.5 5.2 - - + -
144B GLU 2.9 14.5 + - - +
145B PRO* 3.3 3.9 - - + +
146B THR* 2.9 26.0 + - - +
166B ILE* 4.9 0.4 - - + +
167B ILE* 1.3 80.1 - - - +
169B MET* 1.3 64.1 + - - +
189B VAL* 3.2 11.0 - - + +
191B THR* 3.5 29.6 - - + -
203B HIS* 3.6 22.7 - - - +
206B VAL* 4.2 6.5 - - + -
207B ALA* 4.2 13.5 - - + -
210B LEU* 3.8 28.7 - - + -
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Residues in contact with MET 169 (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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146B THR* 3.2 15.9 - - + +
147B SER 3.3 26.2 - - - +
148B GLY* 3.5 13.2 - - - -
167B ILE* 4.5 5.2 - - + -
168B VAL* 1.3 74.8 - - - +
170B PRO* 1.3 68.4 - - + +
173B MET* 3.4 20.0 - - + -
174B SER 5.4 0.2 - - - +
177B LYS* 3.9 10.8 - - + -
178B VAL* 4.8 9.2 - - - -
181B LEU* 3.8 27.1 - - - -
188B ILE* 4.8 3.4 - - + -
189B VAL 2.9 8.4 + - - +
190B ARG* 3.0 37.8 + - - +
191B THR* 3.0 22.8 + - - -
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Residues in contact with PRO 170 (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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146B THR 3.4 15.0 - - - +
169B MET* 1.3 87.0 - - + +
171B GLU* 1.3 53.4 + - - +
172B LYS* 3.1 6.6 + - + +
173B MET* 3.6 29.9 + - + +
190B ARG* 2.7 27.9 + - - -
191B THR* 3.2 19.5 - - - +
192B PRO 5.4 0.7 - - - +
193B THR* 3.8 20.9 - - + -
203B HIS* 4.4 23.1 - - + +
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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