Contacts of the strand formed by residues 45 - 53 (chain A) in PDB entry 3HS0
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 THR 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PHE* 4.7 7.6 - - + -
36A VAL 3.9 5.4 - - - +
37A HIS* 3.3 21.9 + - - +
44A LYS* 1.3 75.4 - - - +
46A LEU* 1.3 64.1 + - - +
47A PHE 3.5 25.4 - - - +
48A GLN* 4.1 19.5 + - + +
71A GLU* 5.8 2.8 - - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL* 2.8 20.6 + - + +
37A HIS 3.5 5.4 - - - -
38A ASP* 3.2 36.3 - - + +
44A LYS* 3.6 16.2 - - + +
45A THR* 1.3 74.6 - - - +
47A PHE* 1.3 59.8 + - + +
66A GLU 4.8 0.4 - - - -
67A ILE* 3.7 31.0 - - + -
68A PRO* 3.9 21.0 - - + +
71A GLU* 4.7 20.8 - - + +
72A VAL* 4.0 24.5 - - + -
82A VAL* 4.4 15.0 - - + -
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Residues in contact with PHE 47 (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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34A ILE* 4.1 5.6 - - + -
35A PHE* 3.3 2.3 - - - -
36A VAL* 2.9 43.0 + - + -
45A THR* 3.5 6.2 - - - +
46A LEU* 1.3 79.9 - - + +
48A GLN* 1.3 82.1 - - - +
49A THR* 3.5 35.9 - - + -
64A THR 3.6 19.1 - - - -
65A ILE* 3.5 32.1 - - + -
66A GLU* 3.5 33.2 - - + +
67A ILE* 5.4 0.7 - - + -
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Residues in contact with GLN 48 (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 ASP* 5.5 3.4 + - - -
34A ILE 3.1 7.9 - - - +
35A PHE* 2.9 40.6 - - + -
45A THR* 4.1 14.3 + - + +
47A PHE* 1.3 89.7 - - - +
49A THR* 1.3 70.7 + - - +
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Residues in contact with THR 49 (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 ASP* 3.8 5.2 - - - +
34A ILE* 3.1 45.7 + - + -
47A PHE* 3.5 27.8 - - + -
48A GLN* 1.3 81.3 + - - +
50A ARG* 1.3 74.9 + - - +
51A VAL* 4.6 5.2 - - + +
63A PRO* 4.7 11.7 - - + -
64A THR 5.4 0.2 - - - +
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.1 47.7 + - + +
32A LEU 3.2 16.4 - - - +
33A ASP* 2.6 43.0 + - - +
49A THR* 1.3 83.7 + - - +
51A VAL* 1.3 66.4 + - - +
52A ASP* 5.4 1.6 - - - +
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Residues in contact with VAL 51 (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 GLN* 3.5 1.9 - - - -
32A LEU* 2.8 49.4 + - + +
34A ILE* 3.7 25.8 - - + -
49A THR* 4.6 7.2 - - + +
50A ARG* 1.3 78.8 - - - +
52A ASP* 1.3 65.3 + - - +
53A MET 3.8 0.7 + - - -
61A VAL* 4.1 23.6 - - + -
63A PRO* 3.9 26.2 - - + -
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LYS 3.6 4.9 - - - +
31A GLN* 2.9 40.9 + - - +
50A ARG* 5.4 2.1 + - - +
51A VAL* 1.3 74.7 - - - +
53A MET* 1.3 60.7 + - - +
54A ASN* 4.0 18.5 + - - +
61A VAL* 3.8 10.4 - - - +
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Residues in contact with MET 53 (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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3A TYR* 5.6 3.1 - - + -
21A VAL* 4.1 20.2 - - + +
22A GLU 4.3 3.1 - - - -
23A ALA* 3.9 17.9 - - + +
29A PRO* 3.4 2.3 - - - +
30A LYS* 2.8 52.8 + - + +
32A LEU* 3.4 32.8 - - + -
51A VAL 3.8 1.6 + - - -
52A ASP* 1.3 70.3 - - - +
54A ASN* 1.3 61.5 + - - +
59A MET* 3.4 54.9 - - + +
61A VAL* 3.5 17.9 - - + -
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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