Contacts of the strand formed by residues 202 - 208 (chain H) in PDB entry 3WBR
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 202 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E MET* 3.6 7.7 - - - +
201E PRO* 2.8 29.8 - - - +
202E GLN* 3.6 1.4 - - - +
100H GLY 3.4 0.9 - - - +
101H MET* 3.4 7.2 - - - +
102H GLN 2.9 28.1 + - - +
107H SER* 4.0 3.1 + - - -
139H SER* 2.8 36.8 + - - +
141H PHE* 3.6 31.6 - - + +
182H ILE* 3.6 20.8 - - + +
196H ILE* 3.8 12.6 - - + -
200H VAL* 3.3 7.6 + - - +
201H PRO* 1.3 84.3 - - - +
203H LYS* 1.3 73.8 + - - +
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Residues in contact with LYS 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E THR* 4.8 3.6 + - - -
101E MET* 3.8 22.4 - - - +
203E LYS* 4.0 25.3 - - - +
98H SER 3.3 6.5 - - - +
99H THR* 3.2 34.1 - - + +
100H GLY 3.2 18.2 - - - +
101H MET* 4.1 7.0 - - + -
135H LYS* 3.8 14.1 - - - +
137H ASN* 5.3 0.2 + - - -
138H SER* 3.2 28.3 + - - +
139H SER 3.2 13.1 + - - +
140H TYR* 3.6 17.3 - - + -
141H PHE* 2.8 22.2 + - - +
202H GLN* 1.3 78.7 - - - +
204H SER* 1.3 63.6 + - - +
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Residues in contact with SER 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ILE* 3.7 2.6 - - - -
98H SER* 2.9 46.8 + - - +
100H GLY 5.2 0.9 + - - -
102H GLN* 5.5 1.0 + - - -
107H SER* 3.5 24.9 + - - -
110H ASN* 5.2 1.2 + - - -
111H CYS* 4.8 1.7 - - - -
118H LEU* 3.6 23.9 - - - +
140H TYR* 4.0 3.9 - - - -
141H PHE* 4.0 9.2 - - - +
203H LYS* 1.3 80.6 - - - +
205H ILE* 1.3 68.3 + - - +
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Residues in contact with ILE 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H TYR* 4.8 7.4 - - + -
96H PHE 3.4 3.8 - - - +
97H ILE* 3.8 18.6 - - + -
111H CYS* 4.3 0.4 - - - -
118H LEU* 3.4 8.3 - - - +
119H VAL* 2.7 60.8 + - + +
130H ILE* 3.8 17.5 - - + -
134H LEU* 3.7 28.7 - - + -
140H TYR* 3.8 10.8 - - + -
141H PHE 3.6 5.2 + - - +
142H LEU* 4.6 1.8 - - + -
183H ILE* 3.7 26.9 - - + -
204H SER* 1.3 79.7 - - - +
206H CYS* 1.3 64.8 + - - +
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Residues in contact with CYS 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H TRP* 4.0 21.1 - - + -
95H TYR* 3.4 7.4 - - - +
96H PHE* 2.8 42.3 + - + +
98H SER* 3.9 20.4 - - - -
110H ASN* 4.9 0.9 - - - -
111H CYS* 2.0 54.3 - - + -
114H MET* 5.3 2.5 - - - -
116H ALA* 4.2 1.3 - - + -
117H ASP 3.2 4.5 - - - +
119H VAL 4.6 0.2 - - - -
204H SER* 5.0 0.7 - - - -
205H ILE* 1.3 77.8 - - - +
207H LYS* 1.3 61.2 + - - +
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Residues in contact with LYS 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ASP* 5.6 3.1 - - - -
93H SER* 4.0 19.1 + - - +
94H CYS 3.3 6.7 - - - +
95H TYR* 3.5 22.4 + - + +
116H ALA* 3.4 2.7 - - - +
117H ASP* 2.8 34.9 + - + +
118H LEU 5.2 0.2 - - - +
119H VAL* 4.0 19.1 - - + -
120H VAL* 2.9 28.4 + - - +
122H ASN* 3.7 15.2 - - - +
126H GLU* 2.7 32.6 + - - +
206H CYS* 1.3 75.5 - - - +
208H MET* 1.3 64.9 + - - +
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Residues in contact with MET 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H PRO* 5.0 11.4 - - + -
87H TRP* 3.9 36.6 - - + -
93H SER* 3.3 5.8 - - - -
94H CYS* 2.6 46.8 + - + +
114H MET 3.4 22.9 - - - +
115H GLY* 3.5 20.9 - - - +
116H ALA* 3.9 7.2 - - + +
207H LYS* 1.3 77.2 - - - +
209H LYS* 1.3 68.8 + - + +
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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