Contacts of the helix formed by residues 194 - 209 (chain A) in PDB entry 2RGZ
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A VAL* 3.6 2.1 - - - +
193A ASP* 1.3 82.0 + - + +
195A ALA* 1.3 62.1 + - - +
196A GLN* 3.6 8.2 + - - +
197A GLN* 2.8 48.5 + - + +
198A PHE* 3.0 21.7 + - - +
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Residues in contact with ALA 195 (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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161A LEU* 3.3 40.8 - - + +
192A VAL* 3.8 8.0 - - + +
194A ASN* 1.3 71.6 - - - +
196A GLN* 1.3 70.0 + - - +
198A PHE* 2.9 15.8 + - - +
199A LYS* 2.9 17.0 + - - +
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Residues in contact with GLN 196 (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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194A ASN* 3.4 7.5 + - - +
195A ALA* 1.3 81.6 - - - +
197A GLN* 1.3 66.1 + - + +
199A LYS* 3.0 27.7 + - - +
200A GLN* 3.6 14.0 + - - +
203A ARG* 5.0 0.5 + - - -
300A HEM 4.0 20.3 + - - +
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Residues in contact with GLN 197 (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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194A ASN* 2.8 38.1 + - + +
196A GLN* 1.3 80.8 - - + +
198A PHE* 1.3 62.1 + - - +
200A GLN* 3.0 31.5 + - + +
201A LEU* 3.2 11.6 + - - +
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Residues in contact with PHE 198 (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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99A PHE* 4.9 9.9 - + - -
102A GLU* 3.5 38.4 - - + -
103A LEU* 3.6 28.9 - - + -
158A MET* 5.3 0.4 - - + -
161A LEU* 3.4 22.0 - - + -
191A ASN 6.0 0.2 - - - -
192A VAL* 4.0 22.7 - - + -
194A ASN 3.0 21.8 + - - +
195A ALA* 2.9 12.0 + - - +
197A GLN* 1.3 76.5 - - - +
199A LYS* 1.3 61.6 + - - +
201A LEU* 3.0 38.9 + - + +
202A TYR* 3.2 16.2 + + - +
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Residues in contact with LYS 199 (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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158A MET* 3.4 56.8 - - + +
161A LEU* 3.8 20.2 - - + -
162A SER* 3.0 23.6 + - - +
195A ALA 2.9 14.6 + - - +
196A GLN* 3.0 23.2 + - - +
198A PHE* 1.3 75.6 - - - +
200A GLN* 1.3 56.7 + - - +
202A TYR* 3.1 4.6 - - - +
203A ARG* 2.8 45.3 + - - +
300A HEM 2.9 37.4 + - + +
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Residues in contact with GLN 200 (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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196A GLN* 3.7 17.3 + - - +
197A GLN* 3.2 24.4 + - - +
198A PHE 3.0 0.8 - - - -
199A LYS* 1.3 75.5 - - - +
201A LEU* 1.3 57.9 + - - +
203A ARG* 2.9 21.3 + - - +
204A ALA* 2.7 37.6 + - - +
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Residues in contact with LEU 201 (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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99A PHE* 3.4 36.8 - - + -
197A GLN 3.2 6.4 + - - +
198A PHE* 3.0 30.6 + - + +
200A GLN* 1.3 76.9 - - - +
202A TYR* 1.3 59.6 + - + +
204A ALA* 3.4 7.4 + - - +
205A ARG* 3.0 55.2 + - - +
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Residues in contact with TYR 202 (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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85A MET* 5.7 0.2 - - - -
97A LEU* 3.7 32.6 + - + +
99A PHE* 3.9 25.6 - + - -
103A LEU* 3.7 29.3 - - + +
150A VAL* 5.1 0.7 - - + -
153A ALA* 3.3 30.0 + - - +
154A TYR* 4.6 7.4 - - + -
157A TYR* 5.1 1.1 - - + -
158A MET* 3.5 38.6 - - + -
198A PHE* 3.2 9.4 + + - +
199A LYS* 3.1 15.5 - - - +
201A LEU* 1.3 81.2 - - + +
203A ARG* 1.3 56.8 + - - +
205A ARG* 3.2 4.8 + - - +
206A MET* 2.8 63.6 + - + +
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Residues in contact with ARG 203 (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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34A SER* 3.7 32.8 + - - +
35A GLU* 5.6 3.1 - - - -
38A LYS* 5.6 3.6 - - - +
154A TYR* 6.4 1.1 - - + -
158A MET* 5.3 4.2 - - - -
196A GLN 5.0 0.2 + - - -
199A LYS* 2.8 52.3 + - - +
200A GLN* 3.5 24.5 + - - +
202A TYR* 1.3 69.9 - - + +
204A ALA* 1.3 62.9 + - - +
206A MET* 3.8 7.5 - - - +
207A ASN* 2.6 37.3 + - - +
300A HEM 2.6 58.7 + - - +
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Residues in contact with ALA 204 (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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200A GLN 2.7 20.5 + - - +
201A LEU* 3.6 9.2 - - - +
203A ARG* 1.3 74.2 - - - +
205A ARG* 1.3 60.1 + - + +
207A ASN* 4.0 7.3 - - - +
208A ALA* 3.2 24.3 + - - +
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Residues in contact with ARG 205 (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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96A PRO* 3.6 37.1 + - + +
97A LEU* 4.9 6.3 - - + -
98A TYR 5.1 0.2 + - - -
99A PHE* 3.0 41.5 - - + -
201A LEU* 3.0 35.4 + - + +
202A TYR* 3.6 5.6 - - - +
203A ARG 3.1 0.2 - - - -
204A ALA* 1.3 77.2 - - + +
206A MET* 1.3 65.5 + - - +
207A ASN 3.1 2.0 - - - -
208A ALA* 3.0 17.4 + - + +
209A LEU* 3.1 17.2 + - - +
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Residues in contact with MET 206 (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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33A LEU* 3.5 20.8 - - + +
34A SER* 4.7 7.4 - - - -
37A LEU* 3.2 35.0 - - + -
97A LEU* 3.6 19.0 - - + +
150A VAL* 3.5 23.1 - - + -
154A TYR* 3.6 20.6 - - + -
158A MET* 5.4 0.7 - - - +
202A TYR* 2.8 49.8 + - + +
203A ARG* 3.3 11.9 + - - +
205A ARG* 1.3 73.1 - - - +
207A ASN* 1.3 66.3 + - - +
209A LEU* 3.4 28.0 - - - +
211A LEU* 4.9 0.3 - - - +
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Residues in contact with ASN 207 (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 ASP* 3.2 30.9 + - + +
33A LEU* 2.9 14.0 + - - +
34A SER* 2.8 41.7 + - - -
203A ARG* 2.6 22.7 + - - +
204A ALA* 4.0 7.1 - - - +
205A ARG 3.1 0.4 - - - -
206A MET* 1.3 75.0 - - - +
208A ALA* 1.3 66.6 + - - +
209A LEU 3.2 9.0 + - - +
216A LYS* 5.6 6.4 + - - +
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Residues in contact with ALA 208 (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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96A PRO* 6.4 1.8 - - + -
204A ALA 3.2 13.8 + - - +
205A ARG* 3.0 14.2 + - + +
207A ASN* 1.3 74.4 - - - +
209A LEU* 1.3 71.2 + - - +
210A ASP* 3.4 1.9 + - - +
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Residues in contact with LEU 209 (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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33A LEU* 4.8 4.0 - - + -
92A PRO 3.7 16.6 - - - +
93A ALA* 3.9 17.7 - - - +
94A PHE* 4.2 0.9 - - - +
96A PRO* 3.6 35.9 - - + +
97A LEU* 3.7 27.1 - - + -
150A VAL* 5.0 2.7 - - + -
205A ARG 3.1 8.9 + - - +
206A MET* 3.4 22.6 - - - +
207A ASN 3.2 9.8 - - - +
208A ALA* 1.3 84.8 - - - +
210A ASP* 1.3 60.2 + - - +
211A LEU* 3.2 30.1 + - + +
216A LYS* 5.9 1.2 - - - -
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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