Contacts of the helix formed by residues 169 - 184 (chain A) in PDB entry 1B4V
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ASP 3.7 2.6 + - - -
168A THR* 1.3 73.1 + - - +
170A TRP* 1.3 82.5 + - + +
171A TYR 3.1 1.7 + - - -
172A LYS* 3.3 25.4 + - + +
175A ARG* 4.5 5.8 - - - +
336A THR 5.2 0.3 - - - +
337A GLY* 5.5 0.7 - - - -
339A HIS* 3.1 46.7 - - + +
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Residues in contact with TRP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A TRP* 4.9 2.2 - + + -
168A THR* 3.1 25.7 - - + +
169A GLU* 1.3 94.1 + - + +
171A TYR* 1.3 62.5 + - + +
172A LYS 3.6 0.7 - - - -
173A PHE* 3.3 10.1 - - - -
204A ALA* 3.9 16.0 + - + +
210A LYS* 4.7 12.1 - - + -
213A LEU* 3.3 75.0 - - + +
215A THR* 6.3 2.0 - - + -
339A HIS* 3.4 60.6 - + + -
340A GLN* 3.6 8.9 - - - -
341A SER* 2.9 29.7 + - - +
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Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 3.7 5.8 - - + -
164A TRP* 3.6 24.7 - + - -
165A PHE* 3.6 37.9 - + + +
168A THR* 3.3 24.5 + - + -
169A GLU 3.1 0.6 - - - -
170A TRP* 1.3 76.7 - - - +
172A LYS* 1.3 66.3 + - - +
173A PHE* 3.1 25.4 - + - -
174A ALA* 3.1 14.2 + - + +
175A ARG* 3.2 19.3 + - - +
197A PHE* 4.1 2.9 - - - -
200A MET* 3.3 19.2 - - - +
341A SER* 3.0 22.3 + - - -
343A ILE* 2.7 29.8 + - - +
345A ALA* 3.5 21.2 - - + +
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLU* 3.3 20.0 + - - +
170A TRP 3.6 0.2 - - - -
171A TYR* 1.3 78.0 - - - +
173A PHE* 1.3 63.3 + - - +
175A ARG* 3.1 29.9 + - + +
176A VAL* 2.9 34.0 + - + +
335A PRO* 2.8 44.6 + - + +
336A THR 3.9 2.5 - - - +
337A GLY* 2.9 30.4 - - - +
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A TRP 3.3 26.0 - - - -
171A TYR* 3.1 29.8 - + - -
172A LYS* 1.3 77.2 - - - +
174A ALA* 1.3 66.6 + - + +
176A VAL* 3.7 2.9 + - - +
177A SER* 3.5 21.1 + - - -
336A THR* 3.2 37.6 + - + +
340A GLN* 3.5 27.4 - - + +
341A SER 4.0 9.6 - - - -
343A ILE 4.7 1.6 - - - -
344A PRO* 4.8 2.2 - - + -
345A ALA 5.3 0.7 - - - -
362A ILE* 3.6 24.3 - - + +
363A ALA 3.9 6.5 - - - -
364A PRO* 3.6 40.6 - - + -
373A VAL 5.9 0.4 - - - +
374A SER* 4.8 0.9 + - - -
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 3.8 24.5 - - + -
171A TYR* 3.1 21.4 + - + +
173A PHE* 1.3 89.4 - - + +
175A ARG* 1.3 59.7 + - - +
177A SER* 3.4 4.5 + - - -
178A ARG* 3.0 26.5 + - - +
346A LEU* 3.7 22.0 - - + +
362A ILE* 4.0 8.6 - - + +
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Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 2.8 40.8 + - + -
166A GLU* 3.3 40.7 + - - +
167A ASP 4.6 2.8 + - - -
168A THR 2.7 32.3 + - - -
169A GLU* 4.5 1.8 - - - +
171A TYR 3.2 11.6 + - - +
172A LYS* 3.1 36.5 + - + +
174A ALA* 1.3 73.1 - - - +
176A VAL* 1.3 67.3 + - + +
178A ARG* 3.3 24.2 + - - +
179A GLU* 3.0 23.9 + - - +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LYS* 2.9 28.0 + - + +
173A PHE 3.9 5.6 - - - +
175A ARG* 1.3 76.2 - - + +
177A SER* 1.3 57.0 + - - +
179A GLU* 3.3 8.1 + - - +
180A GLN* 3.0 34.0 + - + +
330A ASN* 3.5 31.0 - - - +
334A ASN* 4.0 24.2 - - + +
335A PRO 3.5 23.6 - - - +
336A THR* 4.4 6.3 - - + -
374A SER* 4.7 1.1 - - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE 3.5 3.4 + - - -
174A ALA 3.4 2.5 + - - -
175A ARG 3.3 0.6 - - - -
176A VAL* 1.3 75.7 - - - +
178A ARG* 1.3 61.3 + - - +
180A GLN* 3.3 8.0 + - - +
181A ALA* 2.8 33.0 + - - +
328A ARG* 5.4 0.2 - - - +
348A ILE* 5.1 1.1 - - - +
362A ILE* 3.8 35.8 - - - +
374A SER* 3.3 14.0 + - - -
376A TYR* 2.7 34.9 + - - -
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Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 3.7 14.1 - - - -
166A GLU* 2.6 41.8 + - - -
174A ALA 3.0 14.5 + - - +
175A ARG* 3.5 30.4 + - - +
176A VAL 3.3 0.2 - - - -
177A SER* 1.3 76.0 - - - +
179A GLU* 1.3 58.2 + - - +
181A ALA* 3.4 1.9 + - - +
182A GLY* 2.9 26.3 + - - -
186A LEU 4.7 0.9 - - - +
188A THR* 3.4 36.4 - - + +
190A PHE* 5.2 4.0 - - - -
346A LEU* 3.8 12.5 - - + +
362A ILE* 4.5 0.4 - - - +
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG 3.0 12.2 + - - +
176A VAL* 3.5 9.5 - - - +
178A ARG* 1.3 79.1 - - - +
180A GLN* 1.3 89.0 + - - +
182A GLY* 3.3 9.9 + - - -
183A LYS* 3.0 46.3 + - - +
334A ASN* 4.2 9.3 + - - +
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Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A VAL* 3.0 23.3 + - + +
177A SER* 3.7 4.9 - - - +
179A GLU* 1.3 96.6 + - - +
181A ALA* 1.3 61.0 + - - +
183A LYS* 3.3 9.4 + - - +
184A ALA 3.8 2.4 + - - -
328A ARG* 2.8 40.6 + - - +
330A ASN* 4.1 17.3 + - - +
331A HIS* 4.6 2.9 - - - -
334A ASN* 3.2 23.4 + - - +
420A ILE* 3.9 3.8 - - + +
424A ASN* 2.8 51.7 + - - +
426A THR* 3.9 7.1 - - - +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER 2.8 21.3 + - - +
178A ARG* 3.8 5.8 - - - +
180A GLN* 1.3 73.5 - - - +
182A GLY* 1.3 62.9 + - - +
184A ALA* 2.9 15.2 + - - +
186A LEU* 3.0 36.3 + - + +
188A THR* 4.7 2.5 - - + -
348A ILE* 4.2 17.3 - - + -
420A ILE* 4.1 24.8 - - + +
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Residues in contact with GLY 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ARG 2.9 16.1 + - - -
179A GLU* 3.3 4.2 + - - -
180A GLN 3.2 0.4 - - - -
181A ALA* 1.3 77.7 - - - +
183A LYS* 1.3 56.6 + - - +
185A GLY* 3.0 18.4 + - - -
186A LEU 3.4 12.5 + - - -
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLU* 3.0 33.4 + - - +
180A GLN* 3.3 8.9 + - - +
181A ALA 3.2 0.8 - - - -
182A GLY* 1.3 75.5 - - - +
184A ALA* 1.3 58.3 + - - +
185A GLY 3.2 1.6 + - - -
423A ALA* 3.5 20.5 - - + +
424A ASN* 3.4 24.0 + - - +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLN 3.8 1.1 + - - +
181A ALA 2.9 11.8 + - - +
183A LYS* 1.3 76.5 - - - +
185A GLY* 1.3 61.4 + - - +
186A LEU* 3.3 12.9 + - + +
419A ARG* 3.6 46.8 + - + +
420A ILE* 3.9 15.9 - - + -
423A ALA* 3.7 7.4 - - + -
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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