Contacts of the helix formed by residues 193 - 207 (chain A) in PDB entry 6KSF
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 PRO 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.6 33.4 - - + +
127A ASN* 5.1 2.9 - - - +
173A LEU* 4.0 29.6 - - + -
191A PRO 3.8 5.4 - - - +
192A PHE* 1.3 102.8 - - + +
194A SER* 1.3 60.2 + - - +
195A ASP* 3.4 16.2 - - - +
196A LEU* 4.3 3.6 - - + -
197A ALA 3.1 21.5 + - - -
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Residues in contact with SER 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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192A PHE 3.2 5.5 + - - -
193A PRO* 1.3 73.4 - - - +
195A ASP* 1.3 60.6 + - - +
197A ALA* 3.3 8.3 + - - +
198A PHE* 2.9 28.1 + - - +
318A LEU* 5.1 0.6 - - - +
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Residues in contact with ASP 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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80A VAL* 4.8 0.2 - - - +
113A HIS* 4.4 2.9 + - - -
114A TRP* 3.5 22.1 - - + -
117A GLN* 2.9 29.2 + - - -
122A TYR* 3.0 16.6 + - - -
193A PRO* 3.4 13.9 - - - +
194A SER* 1.3 74.9 + - - +
196A LEU* 1.3 74.5 + - - -
198A PHE* 3.2 3.5 + - - +
199A LEU 3.0 18.9 + - - -
318A LEU* 3.5 32.0 - - + +
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Residues in contact with LEU 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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114A TRP* 4.1 8.1 - - + -
122A TYR* 3.6 20.6 - - + +
173A LEU* 4.1 20.2 - - + -
192A PHE* 3.9 21.8 - - + -
193A PRO* 3.5 8.7 + - + +
194A SER 3.4 0.2 - - - -
195A ASP* 1.3 83.2 + - - +
197A ALA* 1.3 54.7 + - - +
199A LEU* 3.4 11.8 + - + +
200A SER* 2.7 47.7 + - - +
217A GLY* 6.0 0.2 - - - -
219A LEU* 4.9 4.3 - - + -
246A PHE* 4.9 0.7 - - + -
341A MET* 3.6 40.4 - - + -
343A VAL* 4.2 12.6 - - + -
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Residues in contact with ALA 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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192A PHE* 3.8 6.2 - - + +
193A PRO 3.1 14.7 + - - +
194A SER* 3.5 13.2 - - - +
195A ASP 3.2 0.2 - - - -
196A LEU* 1.3 76.8 - - - +
198A PHE* 1.3 56.8 + - - +
200A SER* 3.4 1.7 + - - -
201A GLU* 2.9 30.2 + - - +
214A ALA* 3.7 34.1 + - + +
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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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76A ASP* 3.6 28.9 - - - -
79A ARG* 3.7 25.6 - - + -
80A VAL* 3.4 26.9 - - + -
194A SER 2.9 14.4 + - - +
195A ASP* 3.2 10.7 + - - +
197A ALA* 1.3 74.3 - - - +
199A LEU* 1.3 64.7 + - - +
201A GLU* 3.3 15.8 + - - +
202A GLN* 3.0 57.0 + - - +
318A LEU* 4.2 13.0 - - + -
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Residues in contact with LEU 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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80A VAL* 3.8 28.6 - - + +
82A LEU* 3.7 31.9 - - + -
106A PHE* 4.3 5.6 - - + -
114A TRP* 3.9 31.9 - - + +
195A ASP 3.0 12.9 + - - +
196A LEU* 3.7 22.7 - - + +
198A PHE* 1.3 77.0 - - - +
200A SER* 1.3 61.9 + - - +
202A GLN* 3.2 3.8 + - - +
203A VAL* 3.0 30.2 + - + +
246A PHE* 3.8 26.2 - - + -
341A MET* 4.2 5.4 - - + -
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Residues in contact with SER 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 LEU* 2.7 27.0 + - - +
197A ALA* 3.7 4.2 - - - -
199A LEU* 1.3 75.4 - - - +
201A GLU* 1.3 58.4 + - - +
203A VAL 3.3 0.7 + - - -
204A ALA* 2.9 28.1 + - - +
212A PHE* 4.1 7.9 - - - -
214A ALA* 4.2 3.1 - - - -
244A LEU* 3.3 25.3 - - - +
246A PHE* 4.2 6.6 - - - -
343A VAL* 3.6 35.6 - - - +
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Residues in contact with GLU 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 ALA 2.9 18.6 + - - +
198A PHE* 3.3 18.1 + - - +
200A SER* 1.3 75.6 - - - +
202A GLN* 1.3 71.9 + - - +
204A ALA* 3.8 5.2 - - - +
205A THR* 2.9 45.3 + - - +
211A GLY* 5.8 3.6 + - - +
212A PHE* 3.6 29.7 + - + +
214A ALA 6.1 0.4 - - - +
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Residues in contact with GLN 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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72A VAL* 3.4 36.4 - - + +
76A ASP* 3.7 16.3 - - - +
77A ALA* 5.5 0.2 - - - -
80A VAL* 4.1 17.5 - - + -
82A LEU* 4.3 13.7 - - + -
88A TRP* 5.1 1.6 - - + -
198A PHE* 3.0 62.6 + - + +
199A LEU 3.5 6.1 - - - +
201A GLU* 1.3 87.4 + - - +
203A VAL* 1.3 62.8 + - - +
205A THR* 3.4 1.5 + - - -
206A ALA* 2.9 25.1 + - - +
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Residues in contact with VAL 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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82A LEU* 3.9 19.5 - - + -
88A TRP* 4.3 10.8 - - + -
102A ILE* 4.5 11.4 - - + -
199A LEU* 3.0 15.0 + - + +
200A SER 3.3 6.0 + - - +
202A GLN* 1.3 73.8 - - - +
204A ALA* 1.3 63.6 + - - +
206A ALA* 3.2 4.0 + - - +
207A CYS* 3.0 22.0 + - - +
244A LEU* 3.8 16.4 - - + -
246A PHE* 4.1 20.9 - - + -
275A ILE* 4.1 26.2 - - + -
277A VAL* 4.1 13.7 - - + -
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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 SER 2.9 17.4 + - - +
201A GLU 3.8 2.2 - - - +
202A GLN 3.3 0.2 - - - -
203A VAL* 1.3 77.4 - - - +
205A THR* 1.3 63.6 + - - +
207A CYS* 3.0 10.9 + - - -
208A GLY 3.2 0.2 + - - -
209A PHE* 2.9 35.7 + - + +
212A PHE* 3.5 37.2 - - + -
242A PRO* 4.2 7.4 - - + -
244A LEU* 4.3 5.3 - - + +
277A VAL* 5.9 1.3 - - - -
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Residues in contact with THR 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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68A ASN* 4.2 0.9 - - - +
71A SER* 3.7 33.2 - - - +
72A VAL* 4.0 5.8 - - + -
201A GLU* 2.9 29.9 + - - +
202A GLN* 3.8 5.1 - - - -
204A ALA* 1.3 75.1 - - - +
206A ALA* 1.3 63.6 + - - +
208A GLY* 3.0 14.7 + - - -
209A PHE 3.3 13.6 + - - -
210A GLN* 3.8 26.5 + - + +
211A GLY 5.2 2.1 + - - -
212A PHE 5.7 0.2 + - - -
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Residues in contact with ALA 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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67A LEU* 3.3 8.9 - - - +
68A ASN 3.2 33.1 + - - -
72A VAL* 3.9 6.5 - - + +
85A VAL* 4.0 19.7 - - + -
88A TRP* 3.5 33.4 - - + -
202A GLN 2.9 18.5 + - - +
203A VAL 3.5 1.8 - - - +
204A ALA 3.2 0.2 - - - -
205A THR* 1.3 77.0 - - - +
207A CYS* 1.3 58.1 + - - +
208A GLY 3.4 0.3 + - - -
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Residues in contact with CYS 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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65A PHE* 3.7 19.7 - - - -
67A LEU* 3.9 15.5 - - - -
68A ASN* 5.3 1.1 - - - -
100A ILE* 4.1 15.3 - - + -
102A ILE* 3.6 30.7 - - - -
203A VAL 3.0 17.3 + - - +
204A ALA* 3.0 5.5 + - - +
206A ALA* 1.3 76.1 - - - +
208A GLY* 1.3 59.6 + - - +
209A PHE* 3.5 25.4 - - + -
277A VAL* 3.9 17.7 - - + -
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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