Contacts of the helix formed by residues 189 - 206 (chain A) in PDB entry 3F2F
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 VAL 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.1 15.5 - - + -
126A LEU* 3.9 24.7 - - + -
133A ILE* 3.9 12.1 - - + -
136A VAL* 3.9 26.0 - - + -
139A ALA 5.3 0.7 - - - +
141A MET* 3.0 33.4 + - + +
142A ALA* 4.0 0.4 - - - +
143A VAL* 4.1 9.9 - - + -
164A PHE* 4.1 16.6 - - + -
187A VAL 3.8 0.6 + - - -
188A SER* 1.3 71.4 - - - +
190A HIS* 1.3 67.4 + - + +
192A ALA* 3.4 0.7 + - - +
193A PHE* 2.9 27.7 + - - +
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Residues in contact with HIS 190 (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 ILE* 3.2 37.6 - - + +
136A VAL* 4.6 9.9 - - + +
139A ALA 4.8 10.6 + - - -
188A SER* 3.1 12.8 - - - +
189A VAL* 1.3 87.7 - - + +
191A GLU* 1.3 62.2 + - - +
193A PHE* 3.3 5.8 + - - +
194A GLY* 3.1 18.9 + - - -
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Residues in contact with GLU 191 (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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1A MET* 3.4 39.8 - - - +
3A LEU* 4.0 17.0 - - + +
187A VAL* 3.7 30.9 - - + +
188A SER* 3.1 20.5 + - - +
190A HIS* 1.3 72.8 - - - +
192A ALA* 1.3 61.4 + - - +
194A GLY* 3.2 2.6 + - - -
195A LEU* 2.9 26.3 + - - +
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Residues in contact with ALA 192 (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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98A LEU* 3.6 14.5 - - + +
101A LEU* 3.6 20.2 - - + -
143A VAL* 3.8 22.9 - - + -
145A LEU* 5.2 2.2 - - + -
187A VAL* 3.9 13.6 - - + +
188A SER 3.0 13.2 + - - +
189A VAL 3.7 4.5 - - - +
191A GLU* 1.3 77.0 - - - +
193A PHE* 1.3 56.6 + - - +
195A LEU* 3.2 10.5 + - - +
196A GLY* 2.9 23.2 + - - -
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Residues in contact with PHE 193 (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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101A LEU* 3.6 39.2 - - + +
105A ALA* 6.3 1.3 - - + -
128A VAL* 3.9 15.0 - - + -
129A SER 3.9 6.5 - - - -
130A PRO 4.2 4.9 - - - -
131A SER 3.7 11.9 - - - -
132A GLU* 3.6 25.6 - - - -
133A ILE* 3.6 27.8 - - + -
189A VAL 2.9 17.4 + - - +
190A HIS* 3.6 7.6 - - - +
191A GLU 3.2 0.2 - - - -
192A ALA* 1.3 78.0 - - - +
194A GLY* 1.3 57.3 + - - +
196A GLY* 3.2 2.8 + - - +
197A GLN* 3.0 61.1 + - + +
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Residues in contact with GLY 194 (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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3A LEU* 5.4 0.9 - - - -
190A HIS 3.1 13.8 + - - -
191A GLU* 3.2 4.9 + - - -
193A PHE* 1.3 74.4 - - - +
195A LEU* 1.3 64.2 + - - +
197A GLN* 3.3 17.4 + - - +
198A GLU* 3.2 27.9 + - - +
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Residues in contact with LEU 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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3A LEU* 3.8 27.3 - - + +
6A TYR* 4.7 10.8 - - + -
7A ILE* 3.4 36.6 - - + +
98A LEU* 4.2 19.5 - - + -
145A LEU* 3.8 40.6 - - + -
191A GLU 2.9 13.8 + - - +
192A ALA* 3.3 9.0 - - - +
194A GLY* 1.3 73.2 - - - +
196A GLY* 1.3 64.7 + - - +
198A GLU* 3.2 6.0 + - - +
199A PHE* 3.0 23.0 + - + +
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Residues in contact with GLY 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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98A LEU* 4.4 1.8 - - - +
101A LEU* 5.4 2.5 - - - -
102A ILE* 3.6 29.3 - - - +
192A ALA 2.9 13.8 + - - -
193A PHE* 3.2 5.6 + - - -
195A LEU* 1.3 76.6 - - - +
197A GLN* 1.3 57.2 + - - +
199A PHE* 3.3 5.4 + - - +
200A ASN* 2.9 36.5 + - - +
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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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130A PRO 4.6 6.2 + - - +
131A SER* 3.7 15.0 + - - +
193A PHE* 3.0 48.0 + - + +
194A GLY* 3.5 18.5 - - - +
195A LEU 3.2 0.4 - - - -
196A GLY* 1.3 76.8 - - - +
198A GLU* 1.3 65.3 + - - +
200A ASN* 3.3 8.8 + - - +
201A ARG* 2.9 28.4 + - - +
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Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.8 24.5 - - + -
194A GLY 3.2 13.2 + - - +
195A LEU* 3.2 4.2 + - - +
197A GLN* 1.3 79.4 - - - +
199A PHE* 1.3 65.7 + - - +
201A ARG* 2.8 47.7 + - - +
202A HIS* 2.9 33.7 + - + +
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Residues in contact with PHE 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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7A ILE* 4.4 18.0 - - + +
10A LEU* 3.6 38.8 - - + -
11A LEU* 3.5 38.9 - - + +
14A VAL* 4.3 17.5 - - + -
24A LEU* 6.2 0.4 - - + -
98A LEU* 6.4 0.2 - - + -
102A ILE* 3.8 27.8 - - + -
106A LEU* 5.5 0.2 - - + -
195A LEU* 3.0 16.5 + - + +
196A GLY* 3.4 10.5 - - - +
198A GLU* 1.3 78.1 - - - +
200A ASN* 1.3 69.8 + - - +
202A HIS* 3.3 2.8 + - - +
203A LEU* 2.9 51.1 + - + +
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Residues in contact with ASN 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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101A LEU 5.1 0.8 + - - -
102A ILE* 3.0 48.4 + - - +
105A ALA* 3.5 20.0 - - + +
106A LEU* 3.3 22.6 - - + +
196A GLY 2.9 22.1 + - - +
197A GLN* 3.7 7.8 - - - +
199A PHE* 1.3 78.6 - - - +
201A ARG* 1.3 59.8 + - - +
203A LEU* 4.2 3.3 - - - +
204A LEU* 2.8 43.1 + - + +
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Residues in contact with ARG 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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197A GLN 2.9 18.0 + - - +
198A GLU* 2.8 39.0 + - - +
200A ASN* 1.3 75.3 - - - +
202A HIS* 1.3 84.7 + - - +
204A LEU* 4.2 5.2 - - - +
205A GLN* 3.0 51.0 + - - +
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Residues in contact with HIS 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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7A ILE* 4.2 13.4 - - + +
11A LEU* 3.7 28.7 - - + -
198A GLU* 2.9 32.3 + - + +
199A PHE 3.7 1.3 - - - +
201A ARG* 1.3 102.7 + - - +
203A LEU* 1.3 65.7 + - - +
205A GLN* 3.5 20.9 + - - +
206A THR* 3.4 20.4 + - - +
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Residues in contact with LEU 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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11A LEU* 4.0 18.1 - - + +
14A VAL* 4.8 13.0 - - + -
15A ASN* 5.6 8.7 - - + -
20A THR* 6.4 0.2 - - + -
21A ALA* 4.0 25.1 - - + +
24A LEU* 4.2 20.6 - - + -
25A VAL* 5.5 4.5 - - + -
106A LEU* 4.4 23.8 - - + -
199A PHE* 2.9 42.3 + - + +
200A ASN* 3.7 3.8 - - - +
202A HIS* 1.3 77.1 - - - +
204A LEU* 1.3 63.3 + - + +
206A THR* 2.5 28.9 + - + +
207A MET* 3.9 2.3 + - + -
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.1 9.2 - - + -
105A ALA* 5.7 4.7 - - + +
106A LEU* 3.8 29.2 - - + -
200A ASN* 2.8 27.8 + - + +
201A ARG* 4.2 4.7 - - - +
203A LEU* 1.3 73.6 - - + +
205A GLN* 1.3 66.1 + - + +
206A THR 3.1 2.2 - - - -
207A MET* 3.1 44.8 + - + +
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Residues in contact with GLN 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 ARG* 3.0 43.6 + - + +
202A HIS* 3.7 23.7 - - - +
203A LEU 3.2 1.0 - - - -
204A LEU* 1.3 78.3 - - + +
206A THR* 1.3 60.8 + - + +
207A MET 3.2 7.6 + - - +
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Residues in contact with THR 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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11A LEU* 6.3 1.1 - - + -
15A ASN* 4.6 16.4 + - - +
21A ALA* 3.6 16.5 - - - +
22A ASP* 5.0 3.1 - - - +
202A HIS 3.4 15.9 - - - +
203A LEU* 2.5 23.6 + - - +
204A LEU 3.1 0.2 - - - -
205A GLN* 1.3 77.8 - - + +
207A MET* 1.3 61.3 + - - +
208A SER 4.0 0.2 + - - -
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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