Contacts of the strand formed by residues 59 - 67 (chain A) in PDB entry 1TH7
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 GLY 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLU* 4.0 20.2 + - - +
52A GLU 3.3 9.4 - - - -
53A ILE* 4.6 0.9 - - - -
54A GLN* 2.9 6.3 - - - -
58A SER* 1.3 81.4 + - - +
60A LYS* 1.3 65.7 + - - -
61A LYS* 3.6 14.6 + - - +
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Residues in contact with LYS 60 (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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51A GLU* 3.1 2.0 - - - -
52A GLU* 2.7 48.6 + - + +
54A GLN* 2.7 25.6 + - - +
59A GLY* 1.3 70.1 - - - -
61A LYS* 1.3 69.5 + - - +
62A LEU* 2.9 10.1 - - + +
31G GLU* 5.4 8.1 + - - -
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Residues in contact with LYS 61 (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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49A ASP 5.1 5.4 + - - -
50A SER 3.8 6.4 + - - +
51A GLU* 2.8 33.9 + - - +
59A GLY 3.6 12.8 - - - +
60A LYS* 1.3 80.1 - - - +
62A LEU* 1.3 64.6 + - - +
63A GLY 4.9 2.7 - - - +
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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 VAL* 4.1 26.0 - - + -
50A SER* 2.8 19.4 + - - +
51A GLU 4.7 0.2 - - - -
52A GLU* 3.4 28.7 - - + +
60A LYS* 2.9 35.2 - - + +
61A LYS* 1.3 78.1 - - - +
63A GLY* 1.3 61.5 + - - +
64A THR 3.5 0.3 + - - -
65A ILE* 3.8 21.2 - - + +
74G LEU* 4.2 14.8 - - + -
76G SER* 3.1 24.6 + - - +
77G PRO 5.3 0.5 - - - +
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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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47A LEU 3.6 1.2 - - - +
49A ASP* 3.3 14.0 + - - -
50A SER* 2.6 42.0 + - - -
61A LYS* 3.8 2.8 - - - +
62A LEU* 1.3 77.6 - - - +
64A THR* 1.3 58.3 + - - -
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Residues in contact with THR 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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46A VAL* 4.1 17.5 - - + -
47A LEU 3.2 11.4 - - - +
48A SER* 4.0 15.2 - - - +
49A ASP 4.8 0.5 + - - -
62A LEU 3.5 0.8 + - - -
63A GLY* 1.3 72.5 - - - -
65A ILE* 1.3 61.6 + - - +
13G VAL* 4.1 26.2 - - + -
76G SER* 2.9 20.3 + - - -
77G PRO* 3.2 20.5 + - + +
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Residues in contact with ILE 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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32A VAL* 4.3 7.6 - - + -
45A LEU 3.9 0.2 - - - +
46A VAL* 3.2 5.5 - - - +
47A LEU* 2.9 46.8 + - + +
50A SER* 3.6 29.8 - - - +
62A LEU* 3.8 30.5 - - + -
64A THR* 1.3 82.5 - - - +
66A VAL* 1.3 64.8 + - - +
67A ILE* 3.7 28.6 + - + +
74G LEU* 4.4 14.4 - - + -
75G ILE 3.4 6.5 - - - +
76G SER* 3.8 17.5 - - - +
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Residues in contact with VAL 66 (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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44A ASN* 6.0 1.1 - - + -
45A LEU 3.4 11.0 - - - +
46A VAL* 4.3 11.4 - - + +
65A ILE* 1.3 73.1 - - - +
67A ILE* 1.3 62.4 + - - +
68A ARG 4.0 0.5 + - - -
3G MET* 4.8 12.1 - - + -
10G ALA* 4.9 2.0 - - + +
13G VAL* 3.8 32.8 - - + -
14G LEU* 4.2 19.1 - - + -
43G MET* 3.8 30.0 - - + +
74G LEU* 3.2 6.8 - - - +
75G ILE* 2.9 46.4 + - + +
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Residues in contact with ILE 67 (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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24A VAL* 4.6 9.4 - - + -
26A LEU* 3.6 25.4 - - + -
32A VAL* 3.9 19.1 - - + -
43A MET 4.2 0.2 - - - +
44A ASN* 3.4 3.5 - - - +
45A LEU* 2.8 47.5 + - + +
47A LEU* 4.0 16.2 - - + -
65A ILE* 3.7 25.8 - - + +
66A VAL* 1.3 75.0 - - - +
68A ARG* 1.3 73.0 + - - +
69A GLY 3.3 1.0 + - - -
71A ASN* 5.5 0.4 - - + -
72A VAL* 3.9 9.6 - - + -
43G MET* 4.3 3.1 - - - +
73G ILE 3.6 4.3 - - - +
74G LEU* 3.3 21.5 - - + -
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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