Contacts of the helix formed by residues 185 - 201 (chain A) in PDB entry 6FWF
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 ALA 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLY* 5.4 0.3 - - - -
60A ALA* 5.4 5.9 - - - +
184A GLU* 1.3 77.5 + - - +
186A ARG* 1.3 59.6 + - - +
187A GLU 3.2 0.9 - - - -
188A LYS* 2.8 42.0 + - + +
189A LEU* 3.6 2.3 + - - +
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Residues in contact with ARG 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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60A ALA* 6.6 0.2 - - - -
184A GLU* 3.9 21.9 + - - +
185A ALA* 1.3 78.1 - - - +
187A GLU* 1.3 55.1 + - - +
189A LEU* 2.8 42.1 + - + +
190A PHE* 3.3 27.1 - - + -
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Residues in contact with GLU 187 (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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48A LEU* 4.1 6.4 - - - +
149A ILE* 6.0 1.2 - - - +
153A LEU* 3.7 29.4 - - - +
183A GLN* 3.7 24.7 - - + +
184A GLU* 3.7 30.9 - - + +
186A ARG* 1.3 78.2 - - - +
188A LYS* 1.3 56.0 + - - +
190A PHE* 3.4 7.8 + - - -
191A ASP* 2.8 55.3 + - - +
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Residues in contact with LYS 188 (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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52A ASP* 4.9 7.1 + - - +
53A ASP* 3.1 50.8 + - + +
56A ALA* 3.5 27.5 - - + +
57A GLY* 3.6 9.4 - - - +
181A PRO* 5.2 12.8 - - - +
183A GLN* 5.1 3.8 - - + -
184A GLU 3.1 25.8 - - - +
185A ALA* 2.8 25.6 + - + +
187A GLU* 1.3 73.2 - - + +
189A LEU* 1.3 48.7 + - - +
191A ASP* 3.4 6.2 - - - +
192A PHE* 2.8 32.1 + - - +
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Residues in contact with LEU 189 (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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57A GLY* 3.8 22.9 - - - +
60A ALA* 5.1 6.7 - - + -
61A TRP* 4.3 20.6 - - + +
64A THR* 5.2 13.9 - - + +
185A ALA 3.6 2.4 + - - +
186A ARG* 2.8 26.9 + - + +
188A LYS* 1.3 72.5 - - - +
190A PHE* 1.3 75.5 + - + +
192A PHE* 3.2 5.7 + - + +
193A PHE* 2.8 64.6 + - + -
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Residues in contact with PHE 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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87A TRP* 3.7 17.6 - + + -
149A ILE* 6.3 0.2 - - - -
153A LEU* 3.7 29.4 - - + -
156A TYR* 3.4 35.7 - + + -
186A ARG* 3.3 43.0 + - + -
187A GLU* 4.0 7.2 - - - +
189A LEU* 1.3 87.2 - - + +
191A ASP* 1.3 58.2 + - - +
193A PHE* 3.4 30.0 - + - +
194A PHE* 2.8 34.4 + - - +
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Residues in contact with ASP 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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48A LEU 3.2 26.8 - - - +
49A MET* 3.3 37.0 - - + +
53A ASP* 3.8 21.6 - - + +
54A ILE* 4.7 1.8 - - - -
149A ILE* 4.2 9.0 - - - +
183A GLN* 4.7 0.7 - - - +
187A GLU* 2.8 43.4 + - - +
188A LYS* 3.4 7.6 - - - +
190A PHE* 1.3 77.0 - - - +
192A PHE* 1.3 51.9 + - - +
194A PHE* 4.2 0.4 - - - -
195A TRP* 2.8 31.0 + - - +
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Residues in contact with PHE 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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36A TYR* 4.4 4.5 - - - -
54A ILE* 3.5 38.5 - - + +
57A GLY 3.7 15.5 - - - -
58A GLN* 3.9 16.2 - - + -
61A TRP* 3.5 43.3 - + + -
72A VAL* 5.4 3.6 - - + -
188A LYS 2.8 16.0 + - - +
189A LEU* 3.2 9.4 + - + +
191A ASP* 1.3 71.5 - - - +
193A PHE* 1.3 64.7 + + - +
195A TRP* 3.2 28.2 + + - +
196A THR* 2.8 47.7 + - + +
478A ILE* 3.9 16.2 - - + -
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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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61A TRP* 4.0 15.3 - + - -
72A VAL* 4.7 5.2 - - + -
83A TRP* 3.7 46.5 - + + +
87A TRP* 3.7 25.3 - + + -
156A TYR* 4.5 8.7 - + - -
189A LEU* 2.8 51.6 + - + -
190A PHE* 3.4 40.2 - + - +
192A PHE* 1.3 78.6 - + - +
194A PHE* 1.3 51.7 + - - +
196A THR* 2.4 26.3 + - - -
197A SER* 2.8 22.5 + - - -
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Residues in contact with PHE 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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49A MET* 3.7 20.4 - - + -
87A TRP* 3.3 30.2 - + + +
91A GLU* 3.1 38.8 - - + -
141A ILE* 5.3 6.7 - - + -
145A ARG* 3.2 31.0 - - - -
149A ILE* 3.4 48.5 - - + -
152A ILE* 4.7 0.7 - - + -
190A PHE 2.8 21.7 + - - +
191A ASP 3.6 4.5 - - - +
193A PHE* 1.3 72.0 - - - +
195A TRP* 1.3 52.7 + - - +
197A SER* 3.3 1.6 + - - -
198A TRP* 2.8 35.0 + - + +
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Residues in contact with TRP 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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35A PRO 2.5 40.0 + - - -
36A TYR* 3.7 29.0 - + - +
37A PRO* 4.0 8.4 - - + +
49A MET* 4.5 5.2 - - - -
54A ILE* 3.5 39.7 - - + -
73A LEU* 6.1 2.2 - - + -
191A ASP 2.8 16.8 + - - +
192A PHE* 3.3 27.8 - + - +
193A PHE 3.2 0.2 - - - -
194A PHE* 1.3 72.8 - - - +
196A THR* 1.3 90.6 + - + +
198A TRP* 3.8 10.6 - + + +
199A SER* 2.6 55.7 + - - -
478A ILE* 4.3 18.8 - - + -
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Residues in contact with THR 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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72A VAL* 5.0 11.4 - - + +
73A LEU* 5.2 13.9 - - + +
83A TRP 4.0 2.8 + - - -
84A THR* 3.1 26.8 + - - +
192A PHE* 2.8 34.0 + - + +
193A PHE* 2.4 31.4 + - + -
195A TRP* 1.3 94.3 - - + +
197A SER* 1.3 56.6 + - - +
199A SER* 2.9 7.9 + - - -
200A ALA* 2.8 32.4 + - - +
478A ILE* 6.1 0.2 - - + -
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Residues in contact with SER 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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84A THR* 3.5 12.5 + - - +
87A TRP* 2.9 43.6 - - - +
88A LEU* 3.5 21.3 + - - +
91A GLU* 4.5 4.9 - - - -
193A PHE 2.8 11.2 + - - -
194A PHE* 3.4 8.7 - - - -
196A THR* 1.3 74.2 + - - +
198A TRP* 1.3 52.3 + - - +
200A ALA* 3.1 3.4 + - - +
201A SER* 2.8 38.6 + - - -
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Residues in contact with TRP 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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35A PRO* 5.4 8.5 - - + -
37A PRO* 5.5 2.0 - - + -
127A TYR* 4.7 6.2 + - + +
130A GLN* 4.1 2.2 - - - -
131A SER* 3.9 20.9 - - - -
132A ARG* 3.6 51.6 - - + -
139A VAL* 4.1 26.6 - - + +
141A ILE* 5.2 0.4 - - - +
145A ARG* 3.4 36.6 - - - +
194A PHE* 2.8 23.5 + + + +
195A TRP* 4.0 12.1 - + + +
197A SER* 1.3 71.9 - - - +
199A SER* 1.3 76.6 + - - +
201A SER* 3.2 13.3 + - - -
202A THR* 2.7 60.0 + - + +
211A TYR* 4.8 7.2 - + - -
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Residues in contact with SER 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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35A PRO* 5.3 8.3 - - - -
73A LEU* 5.7 2.8 - - - +
195A TRP* 2.6 53.1 + - - -
196A THR* 2.9 17.7 + - - -
198A TRP* 1.3 88.8 - - - +
200A ALA* 1.3 57.8 + - - +
202A THR 4.3 0.7 + - - -
211A TYR* 3.5 34.5 + - - +
212A THR* 4.3 3.6 + - - +
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Residues in contact with ALA 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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73A LEU* 5.5 1.8 - - + -
84A THR* 3.8 18.6 - - + -
88A LEU* 4.8 2.5 - - + -
196A THR 2.8 23.5 + - - +
197A SER 3.5 4.3 - - - +
199A SER* 1.3 75.4 + - - +
201A SER* 1.3 56.9 + - - +
202A THR 3.6 0.9 - - - -
210A THR* 3.3 13.2 + - - +
212A THR* 3.0 32.1 + - + +
215A TRP* 3.1 20.5 - - + +
216A PRO* 4.0 6.5 - - + -
223A ASN* 4.3 1.7 + - - -
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.7 28.5 - - - +
95A TRP* 5.9 0.9 - - - -
127A TYR* 3.9 27.2 - - - +
128A ARG* 4.1 10.4 - - - +
145A ARG* 5.5 2.6 + - - -
197A SER 2.8 28.4 + - - -
198A TRP* 3.2 7.2 + - - -
200A ALA* 1.3 74.4 - - - +
202A THR* 1.3 61.1 + - - +
210A THR* 4.3 8.1 - - - -
221A ILE* 4.1 15.5 - - - -
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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