Contacts of the helix formed by residues 197 - 210 (chain A) in PDB entry 4U7D
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 SER 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A LYS* 3.2 42.6 + - - +
194A ILE 4.5 0.8 - - - +
195A ALA 3.6 2.4 + - - -
196A LYS* 1.3 79.7 - - - +
198A LYS* 1.3 63.0 + - - +
199A MET* 3.7 6.8 + - - +
200A PHE* 3.3 24.5 + - - +
201A MET* 3.5 25.5 + - - +
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Residues in contact with LYS 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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196A LYS 4.3 0.2 - - - -
197A SER* 1.3 70.2 - - - +
199A MET* 1.3 65.3 - - - +
201A MET* 3.4 8.3 + - - +
202A SER* 3.2 21.7 + - - -
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Residues in contact with MET 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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174A HIS* 3.4 31.6 - - + -
197A SER* 3.3 6.7 - - - +
198A LYS* 1.3 79.5 - - - +
200A PHE* 1.3 59.5 + - - +
202A SER* 2.4 28.8 + - - -
203A ARG* 3.3 20.7 + - - +
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Residues in contact with PHE 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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135A LEU* 4.1 14.6 - - + -
161A LEU* 4.1 28.9 - - + -
174A HIS* 4.3 15.5 - + - +
177A MET* 4.0 21.3 - - + -
187A ILE* 4.9 6.7 - - + -
189A VAL* 3.9 23.8 - - + -
193A LYS* 4.5 17.5 - - + +
194A ILE* 4.3 18.4 - - + -
197A SER* 3.3 22.8 + - - +
199A MET* 1.3 77.5 - - - +
201A MET* 1.3 62.9 + - - +
203A ARG* 3.3 4.2 + - - +
204A LEU* 2.9 55.0 + - + +
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Residues in contact with MET 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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193A LYS 5.2 0.4 - - - +
194A ILE* 3.9 36.6 - - + +
197A SER 3.5 13.8 + - - +
198A LYS* 3.4 10.0 + - - +
199A MET 3.4 0.8 - - - -
200A PHE* 1.3 78.6 - - + +
202A SER* 1.3 56.9 + - - +
204A LEU* 3.5 21.8 + - - +
205A GLU* 2.9 27.2 + - - +
240A ILE* 5.0 13.0 - - + +
241A LEU* 5.0 2.9 - - + -
244A GLN* 4.7 14.6 - - + -
245A PHE* 4.2 26.8 - - + -
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Residues in contact with SER 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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198A LYS 3.2 11.0 + - - -
199A MET* 2.4 36.2 + - - -
201A MET* 1.3 75.6 - - - +
203A ARG* 1.3 60.0 + - - +
205A GLU* 3.1 9.2 + - - +
206A LYS* 2.9 40.3 + - - +
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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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174A HIS* 3.5 48.7 + - + +
175A ALA* 5.0 2.4 - - - +
177A MET* 3.6 21.6 - - + +
178A VAL* 3.7 36.5 - - - +
199A MET* 3.3 23.1 + - - +
200A PHE* 3.3 8.0 + - - +
202A SER* 1.3 82.1 + - - +
204A LEU* 1.3 54.3 + - - +
206A LYS* 3.4 21.7 + - - +
207A ALA* 2.8 35.3 + - - +
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Residues in contact with LEU 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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133A PHE* 4.4 9.2 - - + -
135A LEU* 4.2 20.0 - - + -
177A MET* 3.7 13.9 - - + +
194A ILE* 4.6 4.0 - - + -
200A PHE* 2.9 45.2 + - + +
201A MET* 3.5 24.9 - - - +
203A ARG* 1.3 75.9 - - - +
205A GLU* 1.3 53.1 + - - +
207A ALA* 3.6 1.6 - - - +
208A TYR* 2.7 36.6 + - - +
213A PHE* 3.6 35.3 - - + -
241A LEU* 4.9 1.3 - - + -
245A PHE* 4.0 17.5 - - + -
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Residues in contact with GLU 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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201A MET 2.9 15.3 + - - +
202A SER* 3.1 12.0 + - - +
204A LEU* 1.3 75.8 - - - +
206A LYS* 1.3 60.0 + - + +
208A TYR* 3.3 2.8 + - + +
209A GLU* 3.0 51.1 + - + +
244A GLN* 4.1 14.9 - - - +
245A PHE* 4.0 18.4 - - + -
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Residues in contact with LYS 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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178A VAL* 3.9 13.2 - - + -
202A SER* 2.9 26.8 + - - +
203A ARG* 3.6 27.1 - - - +
205A GLU* 1.3 77.1 - - + +
207A ALA* 1.3 57.8 + - - +
209A GLU* 3.2 11.9 + - - +
210A ALA* 2.9 30.6 + - - +
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Residues in contact with ALA 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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133A PHE* 3.9 25.4 - - + -
177A MET* 3.5 27.6 - - + +
178A VAL* 4.3 2.6 - - - +
203A ARG 2.8 21.7 + - - +
204A LEU* 3.6 5.6 - - - +
206A LYS* 1.3 72.3 - - - +
208A TYR* 1.3 58.6 + - - +
210A ALA* 3.3 5.8 + - - -
211A ARG 3.2 3.8 + - - -
212A ARG* 2.9 28.2 + - + -
213A PHE* 3.5 2.9 + - + -
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Residues in contact with TYR 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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204A LEU 2.7 21.7 + - - +
205A GLU* 3.7 6.1 - - + +
206A LYS 3.3 0.2 - - - -
207A ALA* 1.3 73.1 - - - +
209A GLU* 1.3 69.7 + - + +
211A ARG* 3.2 15.8 + - - +
213A PHE* 3.8 32.3 - + + +
244A GLN 4.1 10.8 - - - -
245A PHE* 3.5 42.4 - + + -
246A PRO* 3.4 9.3 - - + +
247A ASN* 2.8 42.1 + - + +
248A ALA* 3.6 18.4 - - + -
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Residues in contact with GLU 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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205A GLU* 3.0 39.2 + - + +
206A LYS* 3.2 11.4 + - - +
208A TYR* 1.3 83.1 - - + +
210A ALA* 1.3 58.3 + - - +
211A ARG* 3.1 12.6 + - - +
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Residues in contact with ALA 210 (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* 5.2 9.2 - - + +
180A LYS* 6.5 0.7 - - + -
206A LYS 2.9 17.7 + - - +
207A ALA* 3.3 7.4 + - - +
209A GLU* 1.3 74.0 - - - +
211A ARG* 1.3 67.5 + - - +
212A ARG* 3.0 24.1 + - + +
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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