Contacts of the strand formed by residues 200 - 209 (chain A) in PDB entry 6VSB
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 TYR 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ASN* 3.2 7.0 - - - +
197A ILE* 2.7 53.3 + - + +
198A ASP* 3.4 27.4 - - + -
199A GLY* 1.3 72.4 - - - +
201A PHE* 1.3 58.5 + - - +
202A LYS* 3.5 7.4 + - + +
228A ASP* 3.1 33.7 - - - +
229A LEU 3.2 3.6 - - - -
230A PRO* 3.5 34.3 - - + -
231A ILE* 5.3 0.2 - - - -
393C THR* 4.4 3.6 + - - -
394C ASN* 3.6 22.5 + - - -
396C TYR* 3.6 22.7 + - - -
516C GLU* 4.3 11.8 - - - +
519C HIS* 5.1 15.3 - - + +
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Residues in contact with PHE 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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86A PHE* 4.3 11.0 - + - -
106A PHE* 3.6 48.7 - + + -
117A LEU* 4.4 8.7 - - + -
119A ILE* 3.6 24.9 - - + -
194A PHE* 4.1 14.1 - + + -
195A LYS 3.5 6.3 - - - -
196A ASN* 3.7 10.1 - - - +
199A GLY 4.3 0.4 + - - -
200A TYR* 1.3 70.2 - - - +
202A LYS* 1.3 61.2 + - - +
203A ILE* 3.7 24.7 + - + +
228A ASP* 4.0 2.2 - - - -
229A LEU* 2.7 28.7 + - + +
231A ILE* 3.8 21.5 - - + +
235A ILE* 3.5 25.1 - - + -
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Residues in contact with LYS 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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39A PRO 5.0 5.9 + - - -
40A ASP* 5.6 4.0 - - - +
41A LYS* 5.5 16.7 - - - +
193A VAL 4.0 0.7 - - - +
194A PHE* 3.7 3.5 - - - +
195A LYS* 2.9 47.2 + - + +
197A ILE* 3.6 28.5 - - + +
200A TYR* 3.5 5.0 - - + -
201A PHE* 1.3 75.3 - - - +
203A ILE* 1.3 60.6 + - - +
204A TYR* 3.7 31.1 + - + +
225A PRO* 6.0 0.2 - - + -
227A VAL 4.2 3.1 - - - -
228A ASP* 3.9 32.8 - - + +
519C HIS 4.7 13.4 + - - -
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Residues in contact with ILE 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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119A ILE* 4.1 16.8 - - + -
128A ILE* 5.5 2.7 - - + -
175A PHE* 4.6 21.8 - - + -
192A PHE* 4.7 7.2 - - + -
193A VAL 3.6 2.2 - - - -
194A PHE* 3.5 24.9 - - + -
201A PHE* 3.8 31.9 - - + +
202A LYS* 1.3 78.2 - - - +
204A TYR* 1.3 69.9 + - - +
225A PRO* 3.3 6.1 - - - +
226A LEU* 2.9 36.9 + - + -
227A VAL* 3.4 19.8 + - + +
229A LEU* 4.4 13.2 - - + -
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Residues in contact with TYR 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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37A TYR* 3.4 34.4 - + + -
38A TYR 3.2 27.7 + - - -
39A PRO 4.2 7.6 + - - -
40A ASP* 5.3 0.7 - - - -
192A PHE* 3.2 4.3 - - - +
193A VAL* 2.5 59.3 + - + +
195A LYS* 4.1 18.9 + - + -
202A LYS* 3.7 46.0 + - + +
203A ILE* 1.3 78.6 - - - +
205A SER* 1.3 63.3 + - - +
223A LEU* 3.7 3.4 - - + +
224A GLU 3.3 4.9 - - - +
225A PRO* 3.4 40.9 - - + +
226A LEU* 5.1 0.4 - - - -
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Residues in contact with SER 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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191A GLU 2.8 18.9 + - - -
192A PHE* 3.5 29.2 - - - -
204A TYR* 1.3 76.9 - - - +
206A LYS* 1.3 75.9 + - - +
207A HIS* 4.7 4.5 + - - -
223A LEU* 3.5 9.0 - - - +
224A GLU* 2.8 36.1 + - - +
226A LEU* 4.1 21.9 - - - +
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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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190A ARG* 3.9 0.2 - - - -
191A GLU* 3.1 29.9 + - + +
205A SER* 1.3 83.7 + - - +
207A HIS* 1.3 93.5 + - - +
208A THR* 4.5 2.7 - - - +
221A SER* 4.1 23.6 - - - +
222A ALA 3.0 24.4 + - - +
223A LEU* 3.9 13.4 - - + +
224A GLU* 3.7 23.2 + - - +
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Residues in contact with HIS 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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175A PHE 3.4 25.0 + - - -
176A LEU* 4.1 17.5 + - + -
188A ASN* 6.2 2.5 - - + -
189A LEU 3.4 5.8 - - - +
190A ARG* 4.9 11.9 - - + -
191A GLU* 6.2 0.2 - - - -
192A PHE* 5.6 4.1 - + - -
205A SER* 4.7 6.1 + - - -
206A LYS* 1.3 103.6 + - - +
208A THR* 1.3 72.5 + - - +
209A PRO* 4.7 2.4 - - + +
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Residues in contact with THR 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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34A ARG* 4.9 11.4 - - - +
188A ASN* 3.5 3.9 - - - +
189A LEU* 2.5 69.1 + - + +
191A GLU* 4.3 9.5 + - - -
206A LYS* 4.5 2.9 - - - +
207A HIS* 1.3 86.2 + - - +
209A PRO* 1.3 82.3 - - + +
210A ILE* 4.7 2.0 - - + -
221A SER* 4.3 15.1 + - - -
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Residues in contact with PRO 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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187A LYS 4.0 1.6 - - - +
188A ASN* 3.9 19.1 - - - +
207A HIS* 4.7 1.3 - - + +
208A THR* 1.3 96.4 - - + +
210A ILE* 1.3 58.8 + - - +
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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