Contacts of the strand formed by residues 71 - 75 (chain A) in PDB entry 1T5A
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 VAL 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLY 6.4 0.2 - - - -
47A ILE 3.3 2.6 + - - +
48A ILE* 3.7 32.5 - - + -
49A CYS 2.9 26.0 + - - -
69A MET* 3.4 8.7 - - - +
70A ASN* 1.3 88.3 - - + +
72A ALA* 1.3 62.9 + - - +
73A ARG 4.0 0.2 - - - -
108A VAL* 4.6 0.7 - - - -
109A ALA* 3.4 21.5 - - + +
111A ALA* 4.0 26.2 - - + -
239A MET* 4.1 19.1 - - + -
241A PHE* 4.8 0.2 - - + -
358A CYS* 5.9 1.6 - - - -
464A HIS* 4.0 19.3 - - + -
465A LEU* 5.5 1.8 - - + +
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Residues in contact with ALA 72 (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 CYS 3.4 4.3 - - - -
51A ILE* 3.8 20.4 - - + -
69A MET* 4.2 9.4 - - - -
71A VAL* 1.3 74.1 - - - +
73A ARG* 1.3 60.7 + - - +
74A LEU* 4.7 3.8 - - + +
91A VAL* 4.2 25.1 - - + -
108A VAL* 4.5 0.9 - - + +
109A ALA 2.8 15.5 + - - +
110A VAL* 3.6 5.7 - - + +
111A ALA 2.8 29.1 + - - +
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Residues in contact with ARG 73 (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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48A ILE* 4.0 14.3 - - + +
49A CYS 2.8 10.8 + - - +
50A THR* 2.8 44.5 + - - +
51A ILE* 2.9 28.6 + - - +
71A VAL 4.0 1.0 + - - -
72A ALA* 1.3 73.3 - - - +
74A LEU* 1.3 64.6 + - - +
75A ASN* 3.6 28.7 + - - +
111A ALA* 3.7 5.8 - - - +
113A ASP* 2.7 55.8 + - + +
241A PHE* 3.8 18.6 - - + -
360A MET* 3.8 18.4 - - - +
362A SER* 3.9 15.4 + - - -
533A OXL 4.0 19.0 + - - -
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Residues in contact with LEU 74 (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 ILE* 4.9 8.5 - - + +
72A ALA* 4.7 5.2 - - + +
73A ARG* 1.3 79.2 - - - +
75A ASN* 1.3 60.8 + - - +
76A PHE* 3.2 28.1 + - + -
84A HIS* 4.1 13.9 - - + +
87A THR* 3.5 37.0 - - + -
88A ILE* 3.4 37.0 - - + +
91A VAL* 6.0 2.2 - - + -
110A VAL* 4.0 14.4 - - + -
111A ALA 2.8 17.2 + - - +
112A LEU* 4.5 1.6 - - + -
113A ASP* 2.9 26.9 + - - +
237A VAL* 5.5 1.3 - - + -
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Residues in contact with ASN 75 (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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50A THR* 4.3 11.2 - - + +
51A ILE 5.2 2.8 + - - +
73A ARG* 3.6 31.6 + - - +
74A LEU* 1.3 69.4 - - - +
76A PHE* 1.3 57.8 + - - +
77A SER* 2.8 36.4 + - - -
78A HIS* 3.4 23.1 + - + +
84A HIS* 3.6 9.0 + - - -
113A ASP* 4.2 6.4 - - - +
534A PO4 3.9 15.0 + - - -
701A K 3.5 10.2 - - - -
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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