Contacts of the strand formed by residues 59 - 63 (chain X) in PDB entry 4LAH
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 ARG 59 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39X HIS 2.9 7.8 + - - +
40X THR* 3.5 24.1 + - - +
41X LEU* 2.8 31.9 + - - +
58X ARG* 1.3 71.9 - - - +
60X ASN* 1.3 61.0 + - - +
61X VAL* 3.8 14.6 - - + +
75X ASP* 2.7 36.6 + - - +
86X LEU* 3.5 29.8 - - - +
87X PRO* 3.7 25.3 + - - +
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Residues in contact with ASN 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41X LEU* 3.8 5.4 - - - +
43X MET* 3.7 22.6 - - + +
48X PHE* 5.8 0.9 - - + -
53X LYS 4.9 0.2 - - - +
54X PRO* 3.4 22.0 - - + +
55X LEU* 2.7 53.1 + - - +
58X ARG* 3.1 16.4 + - - +
59X ARG* 1.3 72.4 - - - +
61X VAL* 1.3 60.5 + - - +
62X VAL* 5.7 0.4 - - + -
73X GLY 4.1 8.6 + - - +
74X VAL* 3.6 9.6 - - + -
75X ASP* 2.8 28.6 + - - +
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Residues in contact with VAL 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40X THR* 3.8 24.5 - - + -
41X LEU 2.8 13.8 + - - +
42X VAL* 3.3 8.9 - - + -
43X MET* 2.9 27.6 + - - +
59X ARG* 3.8 21.1 - - - +
60X ASN* 1.3 77.6 - - - +
62X VAL* 1.3 65.5 + - - +
63X LEU 4.1 0.2 + - - -
75X ASP* 3.3 13.7 - - + +
77X ILE* 3.7 43.3 - - + -
86X LEU* 4.1 14.1 - - + -
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Residues in contact with VAL 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X MET* 3.3 12.8 - - + +
44X GLY 4.3 0.4 - - - -
45X ARG* 3.9 26.9 - - - -
48X PHE* 3.6 31.9 - - + -
60X ASN* 5.3 0.4 - - + -
61X VAL* 1.3 77.2 - - - +
63X LEU* 1.3 65.0 - - - +
64X THR* 4.3 4.0 - - + -
69X PHE* 3.8 23.1 - - + -
74X VAL* 3.5 26.9 - - + -
75X ASP 2.8 9.5 + - - -
76X VAL* 3.5 7.4 - - - +
77X ILE* 3.0 26.7 + - - +
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Residues in contact with LEU 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X VAL* 4.9 3.5 - - + +
43X MET 2.8 15.4 + - - +
44X GLY* 3.7 0.3 - - - -
45X ARG 3.2 23.9 + - - -
61X VAL 4.1 1.0 + - - -
62X VAL* 1.3 70.5 - - - +
64X THR* 1.3 59.3 + - - +
77X ILE* 3.4 20.8 - - + +
78X HIS 3.6 8.1 - - - -
79X SER 3.4 40.4 - - - +
80X ILE* 3.7 27.1 - - + +
83X ILE* 4.8 1.1 - - + -
98X LEU* 3.9 17.9 - - + -
202X NAP 3.3 44.0 - - + +
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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