Contacts of the helix formed by residues 164 - 182 (chain A) in PDB entry 4X6F
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 ASP 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASN* 2.9 24.6 + - + +
163A SER* 1.3 81.0 + - - +
165A THR* 1.3 64.8 + - - +
166A CYS 3.4 0.7 - - - -
167A PRO* 3.2 8.1 - - - +
168A ARG* 2.4 67.3 + - - +
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Residues in contact with THR 165 (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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58A PHE* 4.3 14.2 - - + -
66A LEU* 4.0 26.5 - - + -
160A ASN* 2.9 13.7 + - - +
161A LEU* 3.4 23.0 - - + +
164A ASP* 1.3 73.5 + - - +
166A CYS* 1.3 59.2 + - - +
168A ARG* 3.5 23.2 + - - +
169A PHE* 3.0 26.7 + - - +
301A 3XU 4.1 12.8 - - + -
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Residues in contact with CYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 4.1 14.1 - - - -
101A GLY* 3.7 6.5 - - - -
102A CYS* 2.1 60.2 - - + -
161A LEU 2.8 21.0 + - - +
162A LEU* 3.6 6.5 - - - +
165A THR* 1.3 74.0 - - - +
167A PRO* 1.4 65.8 - - + +
169A PHE* 3.2 2.4 + - - +
170A ILE* 3.0 20.3 + - - +
301A 3XU 3.6 29.8 - - + -
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Residues in contact with PRO 167 (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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102A CYS* 3.5 9.8 - - + -
162A LEU 3.3 18.6 - - - +
163A SER* 3.2 21.8 - - - +
164A ASP 3.2 13.7 - - - +
166A CYS* 1.4 87.9 - - + +
168A ARG* 1.3 63.4 + - + +
170A ILE* 3.1 24.4 - - + +
171A LEU* 3.5 15.3 + - + +
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Residues in contact with ARG 168 (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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58A PHE* 4.3 20.6 - - + -
62A GLU* 5.3 7.9 + - - -
164A ASP* 2.4 47.7 + - - +
165A THR* 3.6 26.2 + - - +
167A PRO* 1.3 78.3 - - + +
169A PHE* 1.3 64.8 + - - +
171A LEU* 3.5 15.1 + - - +
172A GLY* 3.5 8.0 + - - -
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.6 39.9 - + - -
38A HIS* 3.5 24.9 - + - -
54A SER 3.6 8.7 - - - -
55A ARG 4.3 7.6 - - - -
56A GLY* 4.5 2.9 - - - -
58A PHE* 3.6 34.7 - + + -
63A TRP* 3.3 25.8 - + - -
165A THR 3.0 18.5 + - - +
166A CYS 3.2 3.8 + - - +
168A ARG* 1.3 76.8 - - - +
170A ILE* 1.3 60.1 + - - +
172A GLY* 3.1 3.8 + - - -
173A LEU* 2.8 40.1 + - + +
301A 3XU 3.5 24.2 - - + -
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Residues in contact with ILE 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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9A SER* 3.6 18.6 - - - +
10A PHE* 3.4 40.8 - - + +
32A LEU* 4.5 5.2 - - + -
102A CYS* 4.2 11.4 - - - +
103A GLU 5.1 8.1 - - - -
166A CYS 3.0 14.9 + - - +
167A PRO* 3.1 24.0 - - + +
169A PHE* 1.3 80.3 - - - +
171A LEU* 1.3 62.9 + - + +
173A LEU* 4.1 5.6 - - - -
174A LEU* 3.0 47.4 + - + +
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Residues in contact with LEU 171 (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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167A PRO* 3.5 15.0 + - + +
168A ARG* 3.7 9.9 - - - +
169A PHE 3.2 1.0 - - - -
170A ILE* 1.3 85.9 - - + +
172A GLY* 1.3 62.4 + - - +
174A LEU* 4.0 10.4 - - + +
175A ASP* 3.1 25.2 + - - +
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Residues in contact with GLY 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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56A GLY* 3.8 7.9 - - - -
57A ASN* 4.0 23.4 + - - +
58A PHE* 6.1 1.1 - - - -
168A ARG 3.5 6.3 + - - -
169A PHE* 3.1 6.7 + - - -
171A LEU* 1.3 77.9 - - - +
173A LEU* 1.3 56.5 + - - +
175A ASP* 3.9 5.5 - - - +
176A ALA* 2.9 32.7 + - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.6 27.1 - - + -
32A LEU* 3.6 37.5 - - + -
37A THR* 4.6 4.3 - - + +
38A HIS* 4.4 2.7 - - + -
53A TRP* 3.5 34.5 - - + +
54A SER* 3.7 23.6 - - - +
56A GLY* 4.0 6.3 - - - +
169A PHE* 2.8 31.2 + - + +
170A ILE* 3.7 5.8 - - - +
172A GLY* 1.3 76.5 - - - +
174A LEU* 1.3 58.1 + - - +
176A ALA* 3.4 1.7 + - - +
177A GLY* 2.9 26.9 + - - -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER 5.8 3.4 - - - +
32A LEU* 3.9 32.1 - - + -
170A ILE* 3.0 37.1 + - + +
171A LEU* 4.0 11.2 - - + +
173A LEU* 1.3 75.7 - - - +
175A ASP* 1.3 58.7 + - - +
177A GLY 3.3 0.7 + - - -
178A LYS* 2.8 32.1 + - - +
181A LEU* 4.1 14.2 - - + +
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Residues in contact with ASP 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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171A LEU 3.1 17.6 + - - +
172A GLY* 3.9 5.6 - - - +
174A LEU* 1.3 80.3 - - - +
176A ALA* 1.3 65.4 + - - +
178A LYS* 3.1 39.5 + - - +
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Residues in contact with ALA 176 (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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53A TRP* 3.3 39.4 - - + +
56A GLY* 4.1 12.6 - - - +
172A GLY 2.9 18.9 + - - +
173A LEU 3.7 1.1 - - - +
175A ASP* 1.3 79.5 + - - +
177A GLY* 1.3 58.6 + - - +
178A LYS 3.7 0.2 + - - -
179A ALA* 4.9 3.3 + - - +
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Residues in contact with GLY 177 (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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53A TRP* 3.4 32.0 - - - +
173A LEU 2.9 12.5 + - - -
174A LEU 3.6 1.6 - - - -
176A ALA* 1.3 75.7 - - - +
178A LYS* 1.3 64.9 + - - +
179A ALA* 2.9 5.4 + - - -
180A HIS* 2.9 6.9 + - - +
181A LEU* 2.9 28.0 + - - +
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Residues in contact with LYS 178 (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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174A LEU 2.8 12.9 + - - +
175A ASP* 3.1 34.8 + - - +
176A ALA 3.4 0.2 - - - -
177A GLY* 1.3 75.6 - - - +
179A ALA* 1.3 62.8 + - - +
181A LEU* 3.8 6.1 - - - -
182A GLN* 3.0 50.3 + - - +
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Residues in contact with ALA 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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176A ALA 4.9 2.9 + - - +
177A GLY 2.9 1.7 + - - -
178A LYS* 1.3 82.0 - - - +
180A HIS* 1.3 63.4 + - - +
182A GLN* 3.9 1.4 - - - +
183A ARG* 3.3 21.1 + - - +
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Residues in contact with HIS 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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35A LEU* 4.0 30.1 - - + -
51A TRP* 3.8 29.5 - + - -
53A TRP* 3.6 33.4 - + + +
177A GLY 2.9 7.9 + - - +
179A ALA* 1.3 79.2 - - - +
181A LEU* 1.3 68.7 + - + +
183A ARG* 2.8 73.1 + - - +
212A TYR* 3.8 3.3 - + - -
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Residues in contact with LEU 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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32A LEU* 4.1 23.3 - - + -
35A LEU* 3.7 30.1 - - + -
53A TRP* 4.0 5.8 - - + -
174A LEU* 4.1 24.5 - - + +
177A GLY* 2.9 29.0 + - - +
178A LYS* 4.1 4.3 - - - +
180A HIS* 1.3 83.3 - - - +
182A GLN* 1.3 64.1 + - + +
183A ARG 3.4 0.8 - - - +
212A TYR* 3.3 25.9 + - - +
213A PRO* 5.2 4.7 - - - +
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Residues in contact with GLN 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 LYS* 3.0 39.1 + - - +
179A ALA 3.9 2.7 - - - +
181A LEU* 1.3 81.7 - - + +
183A ARG* 1.3 66.0 + - - +
184A GLN* 3.8 13.6 + - - +
213A PRO* 6.3 0.9 - - - -
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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