Contacts of the strand formed by residues 28 - 34 (chain A) in PDB entry 4H1S
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 GLU 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A TRP* 1.3 76.0 - - - +
29A LEU* 1.3 65.5 + - - +
30A THR* 5.2 0.4 - - - +
75A GLU* 4.4 3.3 - - - +
76A PRO* 5.2 4.9 - - + +
77A ASN* 2.8 34.0 + - - +
291A LYS* 3.1 45.3 + - - +
292A ILE 3.2 17.9 - - - +
293A GLU* 3.2 26.4 + - - +
304A HIS* 4.4 8.0 + - - -
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Residues in contact with LEU 29 (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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27A TRP* 3.9 17.9 + - + -
28A GLU* 1.3 74.1 - - - +
30A THR* 1.3 63.8 + - - +
31A ILE* 3.8 30.5 + - + -
77A ASN 3.6 15.5 - - - +
79A LEU* 4.0 20.0 - - + -
166A VAL* 4.0 22.7 - - + -
171A VAL* 4.5 10.5 - - + -
216A ILE* 4.1 14.4 - - + -
290A LEU 3.5 2.1 - - - +
291A LYS* 3.4 3.3 - - - +
292A ILE* 2.8 35.2 + - + +
294A PHE* 4.1 24.2 - - + -
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Residues in contact with THR 30 (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 GLU* 5.0 0.9 + - - +
29A LEU* 1.3 73.3 - - - +
31A ILE* 1.3 61.2 + - - +
32A LEU* 3.7 15.9 + - + -
71A ILE* 4.0 9.6 - - + -
75A GLU* 3.8 9.4 - - - +
77A ASN 2.7 16.9 + - - -
78A VAL* 3.4 10.0 - - + +
79A LEU* 2.9 27.9 + - - +
289A TYR* 3.6 32.1 - - + -
290A LEU 3.7 4.5 - - - +
291A LYS* 3.1 27.2 + - + +
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Residues in contact with ILE 31 (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 LEU* 3.8 23.8 - - + -
30A THR* 1.3 71.6 - - - +
32A LEU* 1.3 68.7 + - - +
33A HIS* 4.0 9.7 - - + -
79A LEU* 3.7 5.4 - - + +
81A LEU* 4.0 22.4 - - + -
216A ILE* 3.5 29.8 - - + -
238A VAL* 4.2 25.1 - - + -
240A VAL* 4.3 12.3 - - + -
288A GLY 3.7 0.2 - - - +
289A TYR* 3.5 4.3 - - - -
290A LEU* 2.8 46.1 + - + +
292A ILE* 4.4 12.3 - - + -
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Residues in contact with LEU 32 (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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30A THR* 3.7 10.8 - - + -
31A ILE* 1.3 73.9 - - - +
33A HIS* 1.3 64.0 + - - +
68A VAL* 4.3 23.3 - - + +
71A ILE* 3.8 28.3 - - + -
78A VAL* 3.6 25.6 - - + -
79A LEU 2.7 17.8 + - - +
80A LEU* 3.8 15.3 - - + -
81A LEU* 2.8 27.2 + - - +
287A LEU* 4.1 8.5 - - + -
288A GLY 3.2 9.0 - - - +
289A TYR* 3.4 33.2 - - + -
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Residues in contact with HIS 33 (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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31A ILE* 4.0 17.0 - - + -
32A LEU* 1.3 76.7 - - - +
34A THR* 1.3 68.7 + - - +
35A ASN* 4.9 2.4 + - - -
80A LEU* 4.9 0.2 - - - -
81A LEU* 3.3 9.0 - - + +
240A VAL* 3.6 29.3 - - + +
241A GLY 5.3 0.4 + - - -
263A TYR* 2.7 25.3 + + - -
278A VAL* 3.6 24.8 - - + +
279A GLN* 3.6 31.7 - - - -
280A ALA* 3.8 7.3 + - + +
287A LEU* 3.8 1.8 - - - +
288A GLY* 2.8 59.6 + - - -
289A TYR 3.8 0.4 - - - -
290A LEU* 4.9 0.7 - - + -
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Residues in contact with THR 34 (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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33A HIS* 1.3 82.1 + - - +
35A ASN* 1.3 64.7 + - - +
37A VAL* 3.9 13.2 - - + -
64A LEU* 4.1 14.6 - - + -
80A LEU* 5.1 0.9 - - + -
81A LEU 3.0 3.9 + - - +
82A ASP* 2.7 23.4 + - - -
83A ALA* 2.8 24.9 + - - +
110A TYR* 2.7 34.9 + - + +
280A ALA* 5.0 2.0 - - - -
284A GLY* 5.7 3.1 - - - -
286A TYR 4.5 11.4 - - - +
287A LEU* 4.0 16.2 - - + -
310A LEU* 6.3 0.2 - - + -
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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