Contacts of the helix formed by residues 170 - 181 (chain B) in PDB entry 4L6V
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ALA 3.0 11.4 + - - +
167B TRP* 3.6 20.5 - - + +
168B PHE 3.2 4.9 - - - +
169B LYS* 1.3 73.2 - - - +
171B ALA* 1.3 58.6 + - - +
172B GLU* 3.5 8.9 + - - +
173B SER* 3.0 33.8 + - - -
174B ARG* 3.3 19.5 + - - +
294B ASN* 5.8 2.6 + - - -
321B TYR* 5.5 0.4 - - - -
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Residues in contact with ALA 171 (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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168B PHE 5.4 1.6 - - - -
169B LYS 2.7 13.4 + - - +
170B ASN* 1.3 71.4 - - - +
172B GLU* 1.3 65.7 + - - +
174B ARG* 3.9 12.1 - - - +
175B LEU* 3.2 32.1 + - + +
301B ILE* 4.8 6.7 - - + -
321B TYR* 4.0 23.1 + - + +
325B ASN* 4.5 11.7 - - + +
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Residues in contact with GLU 172 (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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170B ASN* 3.3 7.3 - - - +
171B ALA* 1.3 79.0 - - - +
173B SER* 1.3 59.9 + - - +
175B LEU* 3.8 0.9 + - - +
176B ASN* 3.6 17.5 + - - -
291B TYR* 3.6 19.4 - - - +
292B ARG* 3.3 22.3 - - + +
299B HIS 3.1 19.7 - - - +
300B SER* 3.9 5.2 + - - -
301B ILE* 2.9 49.7 + - - +
302B LYS 4.4 0.5 + - - -
321B TYR* 3.5 20.6 + - - +
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ASN* 3.0 32.1 + - - -
172B GLU* 1.3 74.1 - - - +
174B ARG* 1.3 65.0 + - - +
175B LEU 3.2 0.6 + - - -
176B ASN* 3.4 2.0 + - - +
177B HIS* 2.9 47.2 + - - -
292B ARG 4.6 0.2 + - - -
293B THR* 4.3 18.2 - - - +
294B ASN* 5.7 1.2 + - - -
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 6.1 1.6 - - - -
167B TRP* 5.8 8.1 - - - -
168B PHE* 2.7 37.4 + - - +
170B ASN 3.3 15.5 + - - +
171B ALA* 3.4 12.0 + - - +
173B SER* 1.3 78.7 - - - +
175B LEU* 1.3 61.7 + - + +
177B HIS* 3.6 3.8 + - - +
178B HIS* 3.1 56.5 + - + +
325B ASN* 5.6 1.6 + - - -
331B GLN* 3.1 33.3 + - - +
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Residues in contact with LEU 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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171B ALA* 3.2 18.6 + - + +
172B GLU 4.0 0.9 - - - +
174B ARG* 1.3 76.0 - - + +
176B ASN* 1.3 65.7 + - - +
177B HIS 3.1 0.2 + - - -
178B HIS* 3.1 6.4 + - + +
179B LEU* 2.9 47.6 + - + +
291B TYR* 3.6 34.1 - - + +
301B ILE* 3.6 31.2 - - + -
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Residues in contact with ASN 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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172B GLU 3.6 8.2 + - - +
173B SER* 3.4 10.4 + - - +
175B LEU* 1.3 78.3 - - - +
177B HIS* 1.3 62.7 + - + +
180B ALA* 3.2 30.1 + - - +
288B GLY* 2.9 31.6 + - - +
289B HIS* 4.1 5.9 - - - +
291B TYR* 2.8 55.1 + - - +
293B THR* 3.8 18.0 + - + +
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Residues in contact with HIS 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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173B SER* 2.9 39.6 + - - +
174B ARG* 4.1 4.3 - - - +
175B LEU 3.1 0.6 - - - -
176B ASN* 1.3 80.3 - - + +
178B HIS* 1.3 64.2 + - + +
180B ALA* 4.9 0.7 - - - -
181B GLY* 2.6 34.7 + - - +
182B LEU 3.2 2.3 + - - -
293B THR* 5.8 3.6 - - + -
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Residues in contact with HIS 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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174B ARG* 3.1 52.1 + - + +
175B LEU* 3.8 6.8 - - + +
177B HIS* 1.3 79.3 - - + +
179B LEU* 1.3 63.4 + - + +
182B LEU* 3.3 32.7 + - + +
183B PHE* 2.9 41.6 + + + -
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Residues in contact with LEU 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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175B LEU* 2.9 33.1 + - + +
178B HIS* 1.3 84.4 - - + +
180B ALA* 1.3 57.8 + - - +
183B PHE* 3.4 15.6 - - + +
184B GLY 3.1 18.0 + - - -
284B PHE* 2.9 32.6 - - + +
287B ALA* 3.9 27.1 - - + +
288B GLY* 3.9 9.6 - - - +
291B TYR* 4.3 21.3 - - + +
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Residues in contact with ALA 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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176B ASN 3.2 18.7 + - - +
177B HIS* 4.9 1.1 - - - -
179B LEU* 1.3 81.2 - - - +
181B GLY* 1.3 58.5 + - - +
184B GLY* 3.1 4.7 - - - -
185B VAL* 2.8 29.6 + - - +
284B PHE 3.7 5.4 - - - -
285B ILE* 3.8 29.7 - - + +
288B GLY* 4.0 4.9 - - - +
289B HIS* 4.8 7.6 - - + +
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Residues in contact with GLY 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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177B HIS* 2.6 18.2 + - - +
180B ALA* 1.3 72.2 - - - +
182B LEU* 1.3 64.8 + - - -
183B PHE 3.1 2.8 + - - -
185B VAL* 3.3 17.5 + - - +
186B SER* 3.1 23.6 + - - -
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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