Contacts of the helix formed by residues 175 - 186 (chain A) in PDB entry 7CAL
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 LEU 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.7 21.1 - - + +
74A ALA* 3.8 18.2 - - + -
171A ARG 5.8 0.4 - - - +
172A LEU* 3.4 24.2 + - + +
173A TRP 3.1 2.4 - - - -
174A ARG* 1.3 73.6 - - + +
176A ARG* 1.3 62.7 + - - +
177A ARG 3.2 2.9 - - - -
178A VAL* 3.1 17.4 + - + +
179A SER* 3.2 13.8 + - - -
207A PHE* 4.1 31.0 - - + -
701A 3PE 3.7 37.8 - - + +
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Residues in contact with ARG 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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133A TYR* 4.6 7.9 + - - -
137A TRP* 3.8 59.7 + - + +
140A PHE* 4.3 14.0 - - + -
141A ASP* 4.1 14.1 - - - +
173A TRP 3.8 16.5 + - - +
174A ARG* 4.7 3.7 - - - +
175A LEU* 1.3 75.8 - - - +
177A ARG* 1.3 101.3 + - + +
178A VAL 3.2 0.4 - - - -
179A SER* 3.8 8.7 - - - +
180A SER* 2.9 36.4 + - - -
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Residues in contact with ARG 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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63A GLU* 5.6 7.9 + - - +
66A LEU* 4.4 20.0 - - + +
67A VAL* 4.2 14.6 - - + +
70A VAL* 4.2 11.2 - - + -
102A PHE* 3.8 34.5 + - - -
105A ASP* 3.5 32.3 + - - +
106A ILE* 6.0 3.2 - - - +
109A THR* 5.6 1.2 - - - +
133A TYR* 5.2 4.0 + - - -
141A ASP* 5.3 4.6 - - - +
174A ARG* 3.7 14.0 + - - +
175A LEU 3.2 1.0 - - - -
176A ARG* 1.3 119.8 - - + +
178A VAL* 1.3 59.8 + - - +
180A SER* 3.8 6.6 + - - -
181A LEU* 3.6 19.9 + - - +
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Residues in contact with VAL 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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67A VAL* 4.0 27.4 - - + +
70A VAL* 3.7 27.6 - - + -
71A ILE* 4.5 9.9 - - + -
175A LEU* 3.1 12.5 + - + +
177A ARG* 1.3 78.4 - - - +
179A SER* 1.3 64.0 + - - +
180A SER 3.3 0.4 - - - -
181A LEU* 3.1 15.9 + - + +
182A PHE* 3.2 35.0 + - + -
701A 3PE 4.2 27.1 - - + -
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Residues in contact with SER 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 LEU 3.2 14.8 + - - -
176A ARG* 3.6 7.6 + - - -
178A VAL* 1.3 77.5 - - - +
180A SER* 1.3 59.2 + - - +
181A LEU 3.5 0.5 + - - -
182A PHE* 3.7 5.6 + - - +
183A ALA* 3.5 18.2 + - - +
200A LYS* 5.6 1.6 - - - -
701A 3PE 3.8 45.1 - - - +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG* 2.9 26.1 + - - -
177A ARG* 3.8 8.8 + - - -
179A SER* 1.3 75.5 - - - +
181A LEU* 1.3 59.3 + - - +
183A ALA* 4.1 10.1 - - - +
184A ARG* 3.8 28.6 + - - +
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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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63A GLU* 5.4 1.3 - - + +
64A MET* 4.2 25.1 - - + -
67A VAL* 3.7 33.0 - - + -
177A ARG 3.6 13.8 + - - +
178A VAL* 3.1 10.3 + - + +
180A SER* 1.3 78.6 + - - +
182A PHE* 1.3 71.8 + - + +
183A ALA 3.2 1.3 - - - -
184A ARG* 3.7 22.2 - - - +
185A LEU* 3.0 54.6 + - + +
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Residues in contact with PHE 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 VAL* 3.2 39.7 + - + +
179A SER* 3.7 5.6 + - - +
181A LEU* 1.3 86.7 - - + +
183A ALA* 1.3 62.2 + - - +
184A ARG 3.3 0.2 - - - -
185A LEU* 4.3 3.3 - - + +
186A GLU* 3.3 32.0 + - - +
196A ILE* 4.3 29.2 - - + +
199A THR* 4.1 37.7 - - + -
200A LYS* 4.0 40.4 - - + -
203A SER* 4.5 10.8 - - - -
701A 3PE 4.3 12.6 - - + -
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Residues in contact with ALA 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 SER 3.5 14.6 + - - +
180A SER* 4.5 8.7 - - - +
181A LEU 3.2 0.6 - - - -
182A PHE* 1.3 80.4 - - - +
184A ARG* 1.3 56.0 + - - +
186A GLU* 3.9 10.5 + - - +
187A LYS* 2.7 37.6 + - - +
200A LYS* 5.9 2.0 - - - +
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Residues in contact with ARG 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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60A ARG* 5.6 7.1 - - - +
63A GLU* 3.7 33.3 + - - +
64A MET* 5.7 3.8 - - - +
180A SER* 3.8 24.3 + - - +
181A LEU* 3.3 24.7 + - - +
182A PHE 3.3 0.4 - - - -
183A ALA* 1.3 78.9 - - - +
185A LEU* 1.3 74.0 + - + +
186A GLU 3.2 1.1 + - - -
187A LYS* 3.4 13.0 + - - +
188A ASP* 3.4 21.0 + - + +
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Residues in contact with LEU 185 (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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64A MET* 6.1 4.9 - - + -
181A LEU* 3.0 41.7 + - + +
182A PHE* 4.5 5.8 - - + +
183A ALA 3.5 0.2 - - - -
184A ARG* 1.3 85.9 - - + +
186A GLU* 1.3 62.8 + - - +
187A LYS 3.3 0.4 - - - -
188A ASP* 3.6 23.0 + - - +
191A PHE* 3.7 46.2 - - + +
192A ASN 4.6 0.9 - - - +
196A ILE* 4.0 34.5 - - + +
310B ARG* 4.2 1.4 + - - -
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Residues in contact with GLU 186 (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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182A PHE 3.3 20.5 + - - +
183A ALA* 4.1 10.1 - - - +
184A ARG 3.2 1.2 - - - -
185A LEU* 1.3 79.8 - - - +
187A LYS* 1.3 54.6 + - + +
192A ASN 5.6 0.4 - - - -
193A TYR* 3.9 25.2 + - + -
196A ILE* 3.8 18.7 - - + +
197A ARG* 2.8 40.8 + - - -
200A LYS* 4.0 10.8 + - - +
701A 3PE 5.4 4.2 - - - -
306B THR* 4.3 16.5 + - + +
310B ARG* 2.4 36.2 + - - +
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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