Contacts of the strand formed by residues 52 - 65 (chain A) in PDB entry 1H8F
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 GLN 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.3 7.3 - - - -
42A ALA* 2.7 32.0 + - - +
44A PRO* 3.6 22.8 - - + +
50A ARG* 3.3 11.3 + - - +
51A PRO* 1.3 79.6 - - - +
53A GLU* 1.3 66.7 + - - +
54A VAL* 3.6 6.6 + - + +
114A TYR* 3.6 23.3 + - + -
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Residues in contact with GLU 53 (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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39A THR* 4.1 19.8 - - + +
40A VAL 3.5 9.9 - - - +
41A VAL* 4.4 15.0 - - + +
52A GLN* 1.3 75.3 - - - +
54A VAL* 1.3 61.1 + - - +
55A SER* 4.4 0.6 + - - -
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Residues in contact with VAL 54 (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 THR 3.8 0.7 - - - +
39A THR* 3.3 1.3 - - - -
40A VAL* 2.7 53.0 + - + +
42A ALA* 4.1 8.1 - - + -
52A GLN* 4.0 11.9 - - + +
53A GLU* 1.3 79.6 - - - +
55A SER* 1.3 65.6 + - - +
56A TYR* 4.8 8.1 - - + -
75A LEU* 3.8 28.3 - - + -
77A ASP* 5.2 4.0 - - - +
114A TYR* 4.0 43.3 - - + +
131A VAL* 6.2 2.2 - - + -
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Residues in contact with SER 55 (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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37A VAL* 4.2 4.8 - - - +
38A THR 3.1 4.9 - - - -
39A THR* 2.6 33.0 + - - +
53A GLU 4.4 0.5 + - - -
54A VAL* 1.3 74.4 - - - +
56A TYR* 1.3 63.8 + - - +
75A LEU* 3.5 5.5 - - - +
76A CYS* 2.8 41.3 + - - +
77A ASP* 3.9 7.8 + - - +
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Residues in contact with TYR 56 (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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36A LYS 4.1 0.2 - - - +
37A VAL* 3.8 0.3 - - - -
38A THR* 2.8 66.5 + - + +
40A VAL* 4.3 17.4 - - + +
54A VAL* 4.8 12.3 - - + -
55A SER* 1.3 77.7 - - - +
57A THR* 1.3 61.9 + - - +
59A THR* 3.3 28.1 + - + +
73A ALA* 3.5 16.6 - - + -
74A LYS 3.2 15.3 - - - +
75A LEU* 4.2 11.0 - - + -
76A CYS* 4.1 4.7 - - - +
82A VAL* 5.6 1.3 - - + -
84A ILE* 3.5 27.6 - - + +
116A PHE* 4.1 16.4 - + - -
129A ASN* 5.6 0.5 + - - -
131A VAL* 5.8 2.7 - - + -
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Residues in contact with THR 57 (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* 3.4 24.0 + - - +
36A LYS 3.2 19.2 + - - -
37A VAL* 4.2 11.9 - - + -
56A TYR* 1.3 77.0 - - - +
58A ASP* 1.3 86.6 + - - +
59A THR* 3.3 4.0 - - - +
73A ALA* 3.5 2.1 - - - -
74A LYS* 2.7 52.0 + - + +
76A CYS* 4.1 12.3 - - - -
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Residues in contact with ASP 58 (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* 4.4 11.8 - - - -
36A LYS 4.4 2.6 + - - -
57A THR* 1.3 102.2 + - - +
59A THR* 1.3 62.8 + - - +
60A LYS* 3.3 18.9 + - - +
72A GLN* 2.8 17.8 + - - +
73A ALA* 3.9 0.8 - - - -
74A LYS* 3.7 22.9 - - + +
81A LEU* 6.4 0.7 - - + -
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Residues in contact with THR 59 (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 LYS* 5.6 2.2 + - - -
38A THR* 4.9 2.6 + - - -
56A TYR* 3.3 35.0 - - + +
57A THR* 4.4 1.7 - - - -
58A ASP* 1.3 74.0 - - - +
60A LYS* 1.3 62.6 + - - +
71A TYR* 3.5 36.1 - - + -
72A GLN 3.6 4.9 - - - -
73A ALA* 3.8 4.1 - - + +
84A ILE* 5.6 1.3 - - + -
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Residues in contact with LYS 60 (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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58A ASP* 3.7 18.5 - - - +
59A THR* 1.3 74.9 - - - +
61A VAL* 1.3 64.8 + - - +
62A ILE* 3.5 14.8 + - + -
71A TYR* 3.2 6.8 - - - -
72A GLN* 2.9 58.6 + - - +
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Residues in contact with VAL 61 (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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60A LYS* 1.3 75.8 - - - +
62A ILE* 1.3 63.5 + - - +
63A GLY 3.5 24.9 - - - +
64A ASN* 5.2 5.2 - - + +
69A VAL* 3.5 16.2 - - + -
70A VAL 3.8 3.4 - - - -
71A TYR* 4.2 21.1 - - + +
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Residues in contact with ILE 62 (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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60A LYS* 3.5 13.9 + - + -
61A VAL* 1.3 77.9 - - - +
63A GLY* 1.3 57.6 + - - +
70A VAL* 2.9 29.4 + - + +
71A TYR 3.6 18.2 - - - +
72A GLN* 3.4 23.3 - - + -
83A ALA* 4.5 2.9 - - + -
134A TYR* 3.4 35.9 - - + +
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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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61A VAL* 3.5 6.9 - - - +
62A ILE* 1.3 82.0 - - - +
64A ASN* 1.3 61.0 + - - -
65A GLY 3.9 2.5 - - - -
69A VAL* 3.3 10.7 - - - +
70A VAL* 2.9 31.9 + - - -
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Residues in contact with ASN 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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61A VAL* 5.2 4.7 - - + +
63A GLY* 1.3 73.3 - - - -
65A GLY* 1.3 66.9 + - - +
68A GLY 3.9 3.4 - - - +
69A VAL* 3.9 26.2 - - - +
271B LYS* 6.0 0.2 + - - -
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Residues in contact with GLY 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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63A GLY 3.9 1.4 - - - -
64A ASN* 1.3 82.6 - - - +
66A SER* 1.3 69.3 + - - +
67A PHE 3.4 2.5 - - - -
68A GLY 2.8 25.5 + - - +
70A VAL* 4.9 6.3 - - - +
271B LYS* 5.4 1.9 + - - -
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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