Contacts of the strand formed by residues 218 - 223 (chain B) in PDB entry 3HN3
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 VAL 218 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLU* 3.9 0.9 - - - -
41B LEU* 2.9 31.8 + - + +
42B ASP* 4.2 4.1 + - - +
45B TRP* 4.1 26.9 - - + -
79B VAL* 4.3 6.8 - - + +
121B LEU* 3.9 13.5 - - + -
122B ARG 3.4 4.5 - - - +
123B ILE* 3.2 37.2 - - + -
214B LEU* 4.1 29.8 - - + -
216B ARG 4.1 7.6 - - - +
217B SER* 1.3 77.4 - - - +
219B LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 6.1 4.0 - - + -
30B PRO* 4.0 28.5 - - + +
38B CYS* 4.1 22.4 - - + -
39B LYS 3.3 13.0 - - - +
40B GLU* 3.9 13.5 - - + -
41B LEU* 4.3 4.0 - - - +
120B VAL 3.9 0.2 - - - +
121B LEU* 3.7 5.5 - - - +
122B ARG* 2.9 58.1 + - + +
217B SER* 4.2 17.9 - - - +
218B VAL* 1.3 79.4 - - - +
220B LEU* 1.3 67.3 + - - +
221B TYR* 4.7 2.2 - - + -
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B CYS* 3.5 0.7 - - - -
39B LYS* 2.7 40.5 + - + +
41B LEU* 4.2 20.8 - - + +
105B VAL* 4.3 8.1 - - + -
107B LEU* 3.6 31.0 - - + -
111B TRP* 3.9 17.2 - - + -
119B VAL* 4.5 3.8 - - + -
120B VAL 3.3 14.1 - - - +
121B LEU* 3.8 19.1 - - + -
153B ILE* 3.7 29.2 - - + -
166B LEU* 3.7 13.9 - - + -
168B ILE* 4.7 0.2 - - + -
219B LEU* 1.3 78.3 - - - +
221B TYR* 1.3 60.7 + - - +
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Residues in contact with TYR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU 5.0 1.8 + - - -
30B PRO* 3.9 33.4 - - + -
31B GLN 6.0 1.1 - - - -
36B ARG* 4.7 12.7 + - + -
37B GLU 3.1 15.9 - - - +
38B CYS* 4.1 13.2 - - + -
111B TRP* 4.8 1.1 - - - -
118B ARG* 4.7 3.5 + - - -
119B VAL* 3.6 3.3 - - - +
120B VAL* 2.8 59.1 + - + +
122B ARG* 3.9 18.6 + - + -
150B GLU* 2.6 37.4 + - - -
219B LEU* 4.7 2.7 - - + -
220B LEU* 1.3 75.9 - - - +
222B THR* 1.3 75.7 + - - +
223B THR* 3.9 20.0 - - + -
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER 4.6 1.7 + - - -
36B ARG* 3.2 22.0 - - - +
37B GLU* 2.9 34.0 + - - +
111B TRP* 3.5 39.7 - - + +
117B THR* 3.6 24.9 - - + -
118B ARG 3.0 9.0 - - - +
119B VAL* 4.3 2.9 - - + -
120B VAL* 5.8 0.2 - - - -
221B TYR* 1.3 80.7 - - - +
223B THR* 1.3 74.1 + - - +
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER 3.8 6.3 - - - -
36B ARG* 3.6 28.9 - - - +
116B ARG 4.0 0.9 - - - +
117B THR* 3.9 2.6 - - - +
118B ARG* 2.8 63.0 + - - +
221B TYR* 3.9 14.8 - - + -
222B THR* 1.3 82.3 - - - +
224B PRO* 1.3 89.7 + - - +
227B TYR* 3.7 7.9 - - + +
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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