Contacts of the strand formed by residues 203 - 208 (chain A) in PDB entry 1Q6X
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 GLN 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A VAL 3.5 1.4 - - - +
199A ALA* 3.3 5.9 - - - -
200A CYS 2.8 36.8 + - - +
201A CYS* 3.4 23.6 + - + +
202A ASN* 1.3 86.5 + - - +
204A PHE* 1.3 61.2 + - - +
205A PHE* 3.7 19.5 - - + -
232A ALA* 4.5 5.8 - - + +
238A ARG* 3.5 12.8 - - + +
239A LEU* 2.9 53.3 + - - +
240A PRO 4.8 0.2 + - - -
374A ARG* 3.0 33.0 + - + +
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Residues in contact with PHE 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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197A ILE* 3.8 21.1 - - + -
198A VAL 3.5 1.6 - - - -
199A ALA* 3.8 24.5 - - + -
202A ASN 3.7 16.8 - - - -
203A GLN* 1.3 72.7 - - - +
205A PHE* 1.3 63.6 + - - +
242A ILE 4.9 2.9 - - - -
243A GLY* 3.9 20.2 - - - -
273A ILE* 4.8 4.0 - - + -
279A LEU* 4.5 6.5 - - + -
310A ALA 4.2 7.6 - - - -
311A ASN 5.1 0.2 - - - -
312A ARG 3.4 29.6 - - - -
313A TRP* 3.7 19.1 - + + -
374A ARG* 3.6 6.1 - - - +
375A LEU* 2.9 49.7 + - + +
377A TRP* 4.4 22.8 - + - +
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Residues in contact with PHE 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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197A ILE* 3.4 10.3 - - - -
198A VAL* 2.9 37.0 + - - +
200A CYS* 5.2 0.9 - - + -
203A GLN* 3.7 24.5 - - + -
204A PHE* 1.3 79.1 - - - +
206A VAL* 1.3 65.2 + - - +
207A LEU 3.6 0.5 + - - -
228A ILE* 3.8 40.6 - - + -
231A MET* 3.9 27.1 - - + -
232A ALA* 3.9 32.5 - - + -
372A PRO* 4.1 8.3 - - + -
373A ARG 3.3 6.7 - - - +
374A ARG* 3.6 43.3 - - + -
375A LEU* 4.7 0.4 - - - +
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Residues in contact with VAL 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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195A HIS* 3.9 11.4 - - + -
196A VAL 4.0 3.1 - - - -
197A ILE* 4.3 8.3 - - + -
205A PHE* 1.3 71.2 - - - +
207A LEU* 1.3 60.8 + - - +
208A ASP* 3.8 22.2 + - - +
272A MET* 3.6 26.9 - - + -
372A PRO* 3.4 10.8 - - - +
373A ARG* 2.7 63.8 + - + +
375A LEU* 3.6 27.4 - - + -
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Residues in contact with LEU 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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131A ILE* 4.1 16.4 - - + -
195A HIS* 3.3 3.6 - - - +
196A VAL* 3.0 54.8 + - + +
198A VAL* 4.0 20.4 - - + -
205A PHE 3.6 0.2 + - - -
206A VAL* 1.3 72.7 - - - +
208A ASP* 1.3 74.4 + - - +
209A VAL* 3.4 2.2 + - + +
216A LEU* 4.7 0.2 - - + -
221A LEU* 4.2 17.3 - - + -
224A GLN* 3.5 36.1 - - + +
225A LEU* 4.3 12.3 - - + -
228A ILE* 4.7 4.9 - - + -
372A PRO* 4.2 11.2 - - + -
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Residues in contact with ASP 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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193A PRO* 3.9 20.6 - - + +
194A GLU 3.5 6.7 - - - +
195A HIS* 3.8 6.4 + - - +
206A VAL* 3.8 21.2 + - - +
207A LEU* 1.3 75.7 - - - +
209A VAL* 1.3 61.6 + - - +
210A VAL 3.4 13.2 - - - +
211A ILE* 4.6 14.4 - - + +
216A LEU* 3.2 24.4 - - - +
224A GLN* 5.6 1.6 + - - +
272A MET* 5.3 1.7 - - - +
370A PRO* 6.2 0.2 - - - +
373A ARG* 5.7 5.4 - - - +
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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