Contacts of the strand formed by residues 218 - 224 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A GLU* 4.0 0.7 - - - -
41A LEU* 2.8 37.7 + - + +
42A ASP* 4.3 4.2 + - - +
45A TRP* 4.1 26.0 - - + -
79A VAL* 4.2 16.2 - - + +
121A LEU* 4.3 6.5 - - + -
122A ARG 3.4 4.9 - - - +
123A ILE* 3.6 35.0 - - + -
214A LEU* 4.3 22.4 - - + -
216A ARG 4.0 8.7 - - - +
217A SER* 1.3 77.0 + - - +
219A LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 219 (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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29A TYR* 6.2 2.7 - - + -
30A PRO* 3.8 29.4 - - + +
38A CYS* 4.3 17.7 - - + -
39A LYS 3.4 13.2 - - - +
40A GLU* 4.0 14.1 - - + -
41A LEU* 4.3 2.9 - - - +
121A LEU* 3.7 6.7 - - - +
122A ARG* 2.9 62.7 + - + +
217A SER* 4.3 13.9 - - - +
218A VAL* 1.3 78.5 - - - +
220A LEU* 1.3 72.5 + - - +
221A TYR* 4.5 2.0 - - + -
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Residues in contact with LEU 220 (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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38A CYS* 3.6 0.5 - - - -
39A LYS* 2.8 38.3 + - + +
41A LEU* 4.2 19.5 - - + +
105A VAL* 4.1 11.7 - - + -
107A LEU* 3.4 33.7 - - + -
111A TRP* 3.9 16.3 - - + -
119A VAL* 4.2 6.1 - - + -
120A VAL 3.2 15.0 - - - +
121A LEU* 3.9 13.7 - - + -
153A ILE* 3.6 31.4 - - + -
166A LEU* 4.0 10.1 - - + -
219A LEU* 1.3 77.4 - - - +
221A TYR* 1.3 62.0 + - - +
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Residues in contact with TYR 221 (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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28A LEU 5.0 1.8 + - - -
30A PRO* 3.9 36.1 - - + -
31A GLN 5.9 1.3 - - - +
36A ARG* 4.6 13.0 + - + -
37A GLU 3.2 15.7 - - - +
38A CYS* 4.3 12.1 - - - -
111A TRP* 4.8 1.1 - - - -
118A ARG* 4.8 3.8 + - - -
119A VAL* 3.7 0.7 - - - +
120A VAL* 2.8 60.1 + - + +
122A ARG* 4.0 17.1 + - + -
150A GLU* 2.6 37.8 + - - -
219A LEU* 4.5 2.5 - - + -
220A LEU* 1.3 76.5 - - - +
222A THR* 1.3 77.0 + - - +
223A THR* 3.8 20.2 - - + -
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Residues in contact with THR 222 (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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35A SER 4.5 2.3 + - - -
36A ARG* 3.2 22.6 - - - +
37A GLU* 3.0 31.5 + - - +
111A TRP* 3.3 45.3 - - + +
117A THR* 3.8 19.7 - - + -
118A ARG 3.1 9.4 - - - +
119A VAL* 4.5 2.7 - - + -
120A VAL* 5.4 0.4 - - - -
221A TYR* 1.3 82.8 - - - +
223A THR* 1.3 72.3 + - - +
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Residues in contact with THR 223 (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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35A SER 3.9 7.4 - - - -
36A ARG* 3.6 29.2 - - - +
117A THR* 3.9 3.3 - - - +
118A ARG* 2.8 57.5 + - - +
120A VAL* 5.3 0.2 - - + -
221A TYR* 3.8 20.6 - - + -
222A THR* 1.3 82.3 - - - +
224A PRO* 1.3 83.7 + - - +
227A TYR* 3.7 8.3 - - + +
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Residues in contact with PRO 224 (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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35A SER* 3.8 9.9 - - - +
116A ARG 3.8 8.3 - - - +
118A ARG* 3.6 2.2 - - - +
223A THR* 1.3 103.0 + - - +
225A THR* 1.3 64.7 + - - +
226A THR 3.3 16.5 + - - +
227A TYR* 3.4 8.7 - - + +
316A VAL* 3.8 20.2 - - + -
317A SER 3.4 26.5 - - - +
318A ASP* 3.2 25.8 - - + +
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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