Contacts of the strand formed by residues 60 - 65 (chain D) in PDB entry 3T30
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 HIS 60 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D LEU* 3.7 25.4 - - + +
55D ALA* 4.4 11.4 - - + +
56D LYS 4.5 5.6 - - - -
58D GLU* 2.8 46.9 + - - -
59D MET* 1.3 77.3 - - - +
61D ARG* 1.3 61.4 + - - +
62D VAL* 5.5 2.2 - - + -
81D ALA 4.0 0.2 - - - +
82D SER* 3.2 4.7 - - - -
83D LEU* 2.8 39.3 + - + +
106D LEU* 4.0 6.7 - - + -
108D ALA* 3.1 4.9 - - - +
109D GLY* 3.8 8.7 - - - -
110D SER 3.4 1.2 + - - -
111D GLY* 2.8 36.9 + - - -
113D VAL* 3.5 22.0 - - + -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D MET* 5.6 0.9 - - - -
60D HIS* 1.3 75.0 - - - +
62D VAL* 1.3 60.6 + - - +
63D GLU* 3.4 17.4 + - - -
79D THR* 2.8 48.2 + - + +
81D ALA 3.3 10.5 - - - +
82D SER* 3.9 12.6 - - - +
106D LEU* 3.6 4.2 - - - +
107D ARG* 2.7 62.2 + - + +
108D ALA* 2.9 14.4 + - + +
52E GLY* 4.3 4.2 - - - -
53E GLU* 2.8 45.2 + - - +
114E PHE* 3.4 36.1 - - - -
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.3 17.7 - - + -
49D ILE* 4.4 10.1 - - + -
60D HIS* 5.5 1.8 - - + -
61D ARG* 1.3 79.2 - - - +
63D GLU* 1.3 71.1 + - - +
79D THR* 3.5 4.5 - - - +
80D ILE* 2.9 45.5 + - + -
81D ALA* 2.8 19.5 + - + +
83D LEU* 5.8 2.0 - - + -
104D PHE* 4.6 1.3 - - + -
105D GLN 3.3 9.4 - - - +
106D LEU* 4.1 16.6 - - + -
113D VAL* 4.2 20.6 - - + -
115D LEU* 4.5 11.4 - - + -
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 3.4 16.7 + - + +
62D VAL* 1.3 78.6 - - - +
64D ILE* 1.3 63.8 + - - +
65D LEU* 5.0 0.2 - - + -
77D PRO* 3.4 29.9 - - + +
78D VAL 3.1 10.5 - - - +
79D THR* 3.8 16.2 + - - +
80D ILE* 4.4 1.3 - - - +
104D PHE* 3.3 5.4 - - - -
105D GLN* 2.8 63.1 + - + +
107D ARG* 3.4 32.9 + - + +
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 5.5 1.3 - - + -
63D GLU* 1.3 77.1 - - - +
65D LEU* 1.3 71.5 + - - +
66D PRO* 3.8 0.9 - - - +
77D PRO* 3.4 3.1 - - - +
78D VAL* 2.7 36.6 + - - +
80D ILE* 3.7 29.6 - - + +
96D VAL* 6.1 0.4 - - + -
98D LEU* 4.0 28.9 - - + -
102D VAL* 3.8 14.4 - - + -
103D THR 3.3 10.5 - - - +
104D PHE* 3.8 18.6 - - + -
18E LEU* 3.4 36.7 - - + +
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D THR* 4.5 4.9 - - + -
63D GLU* 4.2 0.2 - - - +
64D ILE* 1.3 80.0 - - - +
66D PRO* 1.3 78.9 - - + +
77D PRO* 2.7 42.8 - - + -
103D THR* 2.9 41.4 + - + +
105D GLN* 3.4 47.3 - - + +
18E 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