Contacts of the strand formed by residues 199 - 204 (chain A) in PDB entry 1DWQ
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 LYS 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ALA 3.7 20.5 + - - +
99A ALA* 3.9 8.5 - - + +
100A GLY 2.8 25.3 + - - -
197A SER 3.7 4.4 + - - +
198A ILE* 1.3 80.1 - - - +
200A LYS* 1.3 56.7 + - - +
226A ASP* 3.6 22.7 + - - +
257A TYR* 3.3 46.1 + - + -
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Residues in contact with LYS 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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100A GLY 3.3 4.5 - - - -
102A PHE* 3.8 18.6 - - + -
107A LEU* 4.3 3.1 - - + -
195A TYR* 2.9 50.3 + - - +
196A GLY 3.4 12.3 + - - -
198A ILE* 2.8 31.0 + - + +
199A LYS* 1.3 74.7 - - - +
201A VAL* 1.3 62.6 + - - +
223A TYR* 3.4 37.9 + - + -
224A LYS 5.6 1.1 - - - +
225A PRO* 3.6 10.7 - - + +
226A ASP* 2.7 49.8 + - - +
227A LYS 3.3 1.0 + - - -
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Residues in contact with VAL 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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99A ALA* 5.0 1.3 - - + -
100A GLY 3.0 6.4 + - - +
101A VAL* 3.3 19.0 - - + +
102A PHE* 2.8 34.7 + - - +
200A LYS* 1.3 76.4 - - - +
202A TYR* 1.4 53.9 + - - +
203A ILE* 4.6 3.6 - - + -
225A PRO* 4.8 0.2 - - - -
227A LYS* 3.4 12.3 - - + +
229A TYR* 3.6 34.8 - - + -
253A VAL* 3.8 24.0 - - + -
257A TYR* 3.6 31.6 - - + -
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Residues in contact with TYR 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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102A PHE* 3.6 15.0 - - + -
105A SER 3.6 11.8 + - - -
107A LEU* 3.7 28.9 - - + -
201A VAL* 1.4 71.2 - - - +
203A ILE* 1.3 58.4 + - - +
204A TRP* 3.5 27.8 - + + -
216A GLN* 2.7 40.4 + - + -
219A GLN* 2.8 33.9 + - + -
220A ILE* 3.7 24.2 - - + -
225A PRO* 3.9 19.5 - - + +
227A LYS 2.8 9.6 + - - +
228A VAL* 3.3 4.0 - - + +
229A TYR 2.8 31.9 + - - +
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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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77A VAL* 5.7 0.2 - - + -
101A VAL* 3.7 26.7 - - + -
102A PHE 2.8 12.8 + - - +
103A HIS* 4.4 12.8 - - + -
104A ASN* 2.9 24.7 + - - -
201A VAL* 4.6 1.3 - - + -
202A TYR* 1.3 76.3 - - - +
204A TRP* 1.3 66.8 + - - +
229A TYR* 3.2 15.5 - - + +
231A VAL* 4.1 12.3 - - + -
238A LEU* 4.2 10.8 - - + -
246A VAL* 4.7 17.7 - - + -
249A ILE* 3.6 46.9 - - + -
250A LEU* 4.6 8.5 - - + -
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Residues in contact with TRP 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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104A ASN* 3.2 10.3 - - - +
202A TYR* 3.5 21.1 - + + -
203A ILE* 1.3 78.1 - - - +
205A THR* 1.3 71.3 + - - +
206A ASP* 3.7 24.0 - - + -
213A PRO* 3.8 11.9 - - + -
216A GLN* 3.2 47.3 - - + +
217A ARG* 3.7 44.0 - - + -
220A ILE* 4.1 7.0 - - + +
228A VAL* 3.8 16.2 - - + +
229A TYR 3.1 15.2 + - - -
230A GLN* 3.2 39.0 + - + +
231A VAL* 2.8 31.5 + - - +
238A LEU* 4.1 5.2 - - - -
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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