Contacts of the helix formed by residues 170 - 186 (chain B) in PDB entry 4U7C
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 ASN 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A ARG* 5.9 0.5 - - - +
421A THR 3.5 7.1 - - - +
422A PHE* 3.3 28.3 - - + +
423A SER* 3.4 19.4 + - - +
116B GLU* 2.9 25.5 + - - +
167B VAL* 5.1 1.4 - - - +
168B PRO* 3.7 8.9 + - - +
169B PRO* 1.3 75.0 - - - +
171B PHE* 1.3 64.4 + - - +
172B ASP* 3.2 2.9 - - - -
173B LYS* 3.1 36.1 + - + +
174B TYR* 3.2 18.6 + - - -
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TYR* 3.9 16.4 - - - -
169B PRO 3.8 2.4 - - - -
170B ASN* 1.3 72.7 - - - +
172B ASP* 1.3 63.3 + - - +
174B TYR* 3.2 16.7 + + - +
175B ARG* 2.9 57.8 + - - +
197B LEU* 3.9 20.9 - - + -
604B PEG 3.3 25.4 - - - -
5T VKJ 3.7 35.7 - + + -
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Residues in contact with ASP 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ARG* 2.7 45.4 + - + -
422A PHE* 6.1 1.3 - - + -
434A LEU* 4.0 18.8 - - + +
437A GLU* 3.1 34.7 - - - +
438A LEU* 5.9 0.7 - - - -
441A GLU* 4.0 2.3 - - - +
170B ASN 3.1 1.2 + - - -
171B PHE* 1.3 79.3 + - - +
173B LYS* 1.3 66.1 + - - +
175B ARG* 3.2 25.1 + - - +
176B ALA* 2.9 20.6 + - - +
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A PHE* 3.9 8.5 - - + -
423A SER* 3.1 42.8 + - - +
424A GLU 3.2 3.0 + - - -
425A ILE* 3.6 28.7 - - + -
430A GLU* 5.4 2.4 - - - +
434A LEU* 4.0 6.3 - - + +
115B VAL* 4.0 14.4 + - + +
116B GLU* 4.5 1.7 + - - +
118B ARG* 4.6 5.2 - - - +
119B ASP* 2.6 31.7 + - - +
170B ASN* 3.1 30.5 + - + +
172B ASP* 1.3 76.5 - - - +
174B TYR* 1.3 62.8 + - + +
176B ALA* 3.0 7.1 + - - +
177B VAL* 2.9 35.0 + - + +
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Residues in contact with TYR 174 (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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111B PHE* 3.8 18.8 - + + -
112B TYR* 3.7 58.7 + + + -
115B VAL* 4.0 22.7 - - + -
116B GLU* 2.9 34.0 + - - +
130B VAL* 3.6 6.2 - - - +
169B PRO* 3.6 11.9 - - + +
170B ASN 3.2 35.2 + - - -
171B PHE* 3.2 16.8 + + - +
173B LYS* 1.3 77.4 - - + +
175B ARG* 1.3 57.0 + - - +
177B VAL* 4.6 1.8 - - - -
178B SER* 2.9 30.0 + - - -
197B LEU* 4.0 15.8 - - + +
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Residues in contact with ARG 175 (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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437A GLU* 3.2 46.7 + - - +
440A SER* 6.1 1.0 - - - -
441A GLU* 5.2 3.8 + - - +
171B PHE* 2.9 47.6 + - - +
172B ASP* 3.4 23.0 + - - +
173B LYS 3.1 0.2 - - - -
174B TYR* 1.3 76.0 - - - +
176B ALA* 1.3 58.9 + - - +
178B SER* 3.4 6.5 - - - -
179B LYS* 2.9 26.2 + - - +
197B LEU* 4.0 15.9 - - + +
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Residues in contact with ALA 176 (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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430A GLU* 4.0 24.5 - - + +
433A SER* 3.6 31.9 + - - +
434A LEU* 4.9 2.7 - - + +
437A GLU* 3.8 1.5 + - - +
172B ASP 2.9 11.7 + - - +
173B LYS* 3.0 11.2 + - - +
175B ARG* 1.3 73.6 - - - +
177B VAL* 1.3 61.6 + - - +
179B LYS* 2.9 21.9 + - - +
180B GLU* 3.0 18.6 + - - +
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Residues in contact with VAL 177 (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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430A GLU* 3.4 23.6 - - - +
108B MET* 5.6 0.2 - - + -
111B PHE* 3.8 25.4 - - + -
115B VAL* 4.4 11.0 - - + -
118B ARG* 3.8 17.7 - - - +
173B LYS* 2.9 18.9 + - - +
174B TYR* 3.9 4.3 - - - +
176B ALA* 1.3 74.6 - - - +
178B SER* 1.3 64.8 + - - +
180B GLU* 3.1 11.6 + - - +
181B VAL* 3.0 33.0 + - + +
305B THR* 4.5 7.4 - - + -
307B LEU* 3.8 15.0 - - + -
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Residues in contact with SER 178 (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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111B PHE* 4.5 1.1 - - - -
174B TYR 2.9 20.7 + - - -
175B ARG 3.4 6.5 - - - -
177B VAL* 1.3 77.9 - - - +
179B LYS* 1.3 55.4 + - - +
181B VAL* 3.4 6.0 + - - +
182B LYS* 2.9 48.9 + - - +
196B SER 4.6 1.2 + - - -
197B LEU* 3.1 50.1 + - - +
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Residues in contact with LYS 179 (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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429A GLU* 4.4 8.7 - - - +
433A SER* 3.2 26.0 - - - +
436A GLN* 4.0 20.4 + - - +
175B ARG 2.9 12.3 + - - +
176B ALA* 2.9 12.4 + - - +
178B SER* 1.3 76.4 - - - +
180B GLU* 1.3 56.5 + - + +
182B LYS* 3.4 10.5 + - - +
183B GLU* 2.9 54.0 + - + +
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Residues in contact with GLU 180 (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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427A LYS* 4.4 6.8 - - - +
429A GLU* 3.4 42.5 - - + +
430A GLU* 2.9 40.2 + - + +
433A SER* 6.0 0.2 - - - +
176B ALA 3.0 11.5 + - - +
177B VAL* 3.4 14.2 - - - +
179B LYS* 1.3 76.4 - - + +
181B VAL* 1.3 62.3 + - - +
183B GLU* 3.0 7.2 + - - +
184B ILE* 3.0 19.8 + - - +
304B LYS* 3.4 30.1 + - - +
305B THR* 4.0 21.9 - - + +
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Residues in contact with VAL 181 (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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106B ILE* 6.3 1.1 - - + -
108B MET* 4.3 27.6 - - + -
111B PHE* 6.0 0.2 - - + -
177B VAL* 3.0 26.8 + - + +
178B SER* 3.8 6.5 - - - +
180B GLU* 1.3 75.4 - - - +
182B LYS* 1.3 60.3 + - + +
184B ILE* 3.0 12.0 + - - +
185B LEU* 2.9 40.8 + - + +
197B LEU 5.8 2.2 - - - +
301B ILE* 4.0 27.8 - - + -
305B THR* 4.0 18.4 - - + +
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Residues in contact with LYS 182 (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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178B SER* 2.9 36.1 + - - +
179B LYS* 3.7 7.6 - - - +
181B VAL* 1.3 75.7 - - + +
183B GLU* 1.3 55.7 - - - +
185B LEU* 3.2 12.6 + - + +
186B ALA* 2.9 31.4 + - - +
192B PHE* 4.1 25.6 - - + -
194B ALA* 4.9 14.1 - - + -
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Residues in contact with GLU 183 (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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429A GLU* 2.8 27.3 - - - +
179B LYS* 2.9 40.6 + - + +
180B GLU 3.1 9.9 - - - +
182B LYS* 1.3 76.8 - - - +
184B ILE* 1.3 62.1 + - - +
186B ALA* 3.4 14.6 + - - +
187B ASP* 4.0 7.8 + - - +
300B ARG* 5.3 0.2 + - - -
304B LYS* 2.7 30.2 + - - +
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Residues in contact with ILE 184 (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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180B GLU 3.0 14.3 + - - +
181B VAL* 3.0 9.8 + - - +
183B GLU* 1.3 75.9 - - - +
185B LEU* 1.3 63.1 + - + +
187B ASP* 3.1 22.7 + - - +
188B TYR* 3.6 7.5 - - + -
297B ILE* 4.1 24.7 - - + +
300B ARG* 3.4 69.8 - - + +
301B ILE* 3.4 16.2 - - + +
304B LYS* 3.9 24.7 - - + +
305B THR* 5.5 1.1 - - + -
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Residues in contact with LEU 185 (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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106B ILE* 3.7 33.7 - - + -
181B VAL* 2.9 34.3 + - + +
182B LYS* 3.6 12.8 - - + +
184B ILE* 1.3 73.3 - - + +
186B ALA* 1.3 60.0 + - - +
187B ASP 3.1 1.5 + - - -
188B TYR* 3.3 5.3 + - - +
189B ASP 3.3 20.6 + - - +
192B PHE* 4.1 17.6 - - + -
200B ALA* 3.8 29.2 - - + -
202B LEU* 3.9 20.2 - - + +
297B ILE* 3.8 16.6 - - + -
301B ILE* 4.8 6.7 - - + -
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Residues in contact with ALA 186 (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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182B LYS 2.9 15.9 + - - +
183B GLU* 3.8 8.5 - - - +
184B ILE 3.1 0.8 + - - -
185B LEU* 1.3 78.1 - - - +
187B ASP* 1.3 62.4 + - - +
188B TYR 3.3 0.6 + - - -
189B ASP 3.6 10.1 - - - +
190B PRO* 3.6 25.4 - - + +
192B PHE* 4.4 10.7 - - + -
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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
------------------------------------------------------------
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