Contacts of the strand formed by residues 203 - 210 (chain C) in PDB entry 3WHD
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 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C ASP 3.6 0.7 - - - +
102C ASN* 3.1 14.1 - - - +
103C LYS 3.0 29.8 + - - +
108C SER* 4.5 1.2 + - - -
140C SER* 3.6 25.8 - - - +
142C PHE* 3.7 23.1 - - + -
184C VAL* 4.3 6.5 - - + -
197C VAL* 6.2 0.2 - - + -
201C PHE* 6.2 0.2 - - + -
202C GLU* 1.3 76.3 - - - +
204C SER* 1.3 66.5 + - - +
205C ARG* 5.0 0.2 + - - -
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Residues in contact with SER 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU 3.2 14.6 - - - -
100C THR* 2.8 24.1 + - - -
101C ASP 4.0 6.1 - - - -
102C ASN* 3.6 3.2 + - - -
139C LEU* 3.7 15.8 - - - +
140C SER 2.9 15.3 + - - -
141C TYR* 3.7 15.9 - - - -
142C PHE* 2.8 26.0 + - - +
203C ALA* 1.3 80.4 - - - +
205C ARG* 1.3 65.8 + - - +
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Residues in contact with ARG 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PRO* 3.3 2.4 - - - +
99C LEU* 2.7 69.0 + - + +
101C ASP* 2.9 53.7 + - - -
103C LYS* 3.6 21.5 - - - +
108C SER* 3.6 41.7 + - - +
111C ASN* 2.9 31.4 + - - +
112C CYS* 4.5 4.0 - - - -
119C LEU* 4.0 9.9 - - + -
141C TYR* 3.7 2.9 - - - -
142C PHE* 3.9 8.7 - - + +
204C SER* 1.3 78.1 - - - +
206C ILE* 1.3 64.9 + - - +
207C CYS* 4.7 2.5 - - - -
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Residues in contact with ILE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 4.4 1.1 - - + -
97C PHE 3.6 11.4 - - - +
98C PRO* 4.3 6.5 - - + -
112C CYS* 4.4 0.9 - - - -
119C LEU* 3.5 6.8 - - - +
120C MET* 2.8 54.3 + - + -
131C ILE* 3.8 35.2 - - + -
135C LEU* 4.0 7.6 - - + -
141C TYR* 3.9 27.6 - - + -
142C PHE 3.5 8.0 + - - +
143C LEU* 4.2 6.1 - - + -
185C LEU* 4.1 17.9 - - + -
205C ARG* 1.3 80.4 - - - +
207C CYS* 1.3 70.5 + - - +
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Residues in contact with CYS 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C TRP* 3.8 20.8 - - + -
96C TYR* 3.3 6.9 - - - +
97C PHE* 2.9 36.6 + - + +
99C LEU* 4.1 12.8 - - - -
111C ASN* 4.6 1.1 - - - -
112C CYS* 2.1 54.5 - - + -
115C MET* 3.4 15.7 - - + -
117C ALA* 4.1 1.8 - - + -
118C HIS 3.4 4.3 - - - -
205C ARG* 4.7 2.2 - - - -
206C ILE* 1.3 75.6 - - - +
208C LYS* 1.3 61.2 + - - +
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Residues in contact with LYS 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C TRP* 4.1 0.9 - - - -
94C ASN* 3.8 25.9 - - + +
95C CYS 3.3 6.1 - - - +
96C TYR* 3.5 29.4 - - + -
117C ALA* 3.3 4.0 - - - +
118C HIS* 2.7 39.6 + - + +
119C LEU 4.9 0.4 - - - +
120C MET* 3.9 10.1 - - - -
121C THR* 3.3 35.8 + - - +
123C SER* 5.6 1.0 + - - -
127C GLU* 2.8 26.6 + - - -
158C ASP* 4.9 7.0 + - - +
207C CYS* 1.3 75.2 - - - +
209C ILE* 1.3 64.7 + - - +
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Residues in contact with ILE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C MET* 5.9 0.7 - - - -
61C HIS* 3.9 16.4 - - + +
85C PRO* 4.4 11.4 - - + -
88C TRP* 3.7 22.0 - - + -
94C ASN* 3.7 2.8 - - - +
95C CYS* 2.8 43.7 + - + -
115C MET 3.8 16.6 - - - +
116C GLY* 3.3 27.4 - - - +
117C ALA* 4.1 2.2 - - + -
208C LYS* 1.3 77.4 - - - +
210C PRO* 1.3 85.7 - - + +
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Residues in contact with PRO 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C SER 4.7 0.7 - - - +
94C ASN* 3.5 18.4 - - - +
95C CYS* 4.3 0.4 - - - -
116C GLY 5.4 0.4 - - - +
208C LYS 5.0 0.2 - - - +
209C ILE* 1.3 106.0 - - + +
211C GLY* 1.3 68.0 + - - +
212C THR* 5.1 2.4 - - - +
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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