Contacts of the strand formed by residues 61 - 66 (chain A) in PDB entry 1H3H
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 LYS 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.4 21.3 - - + +
36A GLY 5.9 2.0 - - - +
38A ARG* 6.3 0.7 - - - +
57A ARG* 2.9 5.9 - - - +
58A LEU* 2.8 41.3 + - + +
59A HIS* 3.8 0.9 - - + -
60A ASN* 1.3 82.9 - - + +
62A LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 62 (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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32A GLU 5.3 1.4 - - - +
33A ASP 4.7 1.9 - - - +
34A GLU 3.9 6.4 - - - +
35A LEU* 4.4 2.7 - - - -
46A LEU* 4.5 7.4 - - + -
55A THR* 6.4 0.9 - - + -
56A GLY 4.4 1.8 - - - +
57A ARG* 3.4 44.4 - - + +
60A ASN 4.5 9.6 - - - +
61A LYS* 1.3 75.6 - - - +
63A GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 63 (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 3.4 8.1 - - - -
34A GLU 3.3 16.8 - - - -
35A LEU* 3.5 12.2 - - - +
55A THR* 4.8 3.0 - - - +
56A GLY 2.6 36.1 + - - +
62A LEU* 1.3 75.6 - - - +
64A LEU* 1.3 68.1 + - - -
65A PHE* 4.9 0.5 - - - +
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Residues in contact with LEU 64 (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* 3.1 34.1 - - + +
34A GLU* 3.2 27.3 - - + +
35A LEU 2.8 23.2 + - - +
53A TRP* 3.5 13.9 - - + -
54A TRP 3.5 9.9 - - - +
55A THR* 3.5 26.9 - - + +
63A GLY* 1.3 74.6 - - - -
65A PHE* 1.3 58.8 + - - +
84B LYS* 3.7 25.6 - - + -
85B PRO* 4.2 12.1 - - + -
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Residues in contact with PHE 65 (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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20A TRP 4.6 0.7 - - - -
21A ALA* 3.4 16.2 - - + -
35A LEU* 4.3 6.5 - - + +
37A PHE* 3.3 31.0 - + + -
43A VAL* 5.6 2.5 - - + -
45A VAL* 3.5 26.0 - - + -
53A TRP* 3.2 16.9 - - - -
54A TRP* 3.1 69.7 + + + -
56A GLY* 4.6 9.4 - - - -
63A GLY 4.9 1.6 - - - +
64A LEU* 1.3 76.4 - - - +
66A PRO* 1.3 85.4 - - + +
67A ALA* 3.3 16.6 + - + -
70A VAL* 3.4 17.5 - - + -
72A PRO* 6.3 0.2 - - + -
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Residues in contact with PRO 66 (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* 3.8 18.6 - - + +
29A ALA 5.0 2.5 - - - +
35A LEU 5.1 1.1 - - - +
37A PHE* 3.5 17.9 - - + -
53A TRP* 3.8 8.7 - - + -
65A PHE* 1.3 96.0 - - + +
67A ALA* 1.3 59.5 + - - +
68A ASN 2.9 8.1 + - - -
69A TYR* 3.1 29.4 + - + -
70A VAL 3.2 6.8 + - - -
79B ILE* 3.4 40.8 - - + -
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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