Contacts of the strand formed by residues 72 - 77 (chain d) in PDB entry 5KZ5
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 72 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380P ALA* 3.4 34.1 - - + -
385P SER* 3.8 7.6 - - - +
386P LEU* 3.2 33.9 - - - +
387P GLU 4.4 0.7 - - - +
71d ASP* 1.3 76.4 - - - +
73d MET* 1.3 68.1 + - - +
74d LYS 3.4 0.5 + - - -
92d THR* 2.9 30.0 + - + +
93d PHE* 3.5 27.4 - - - +
94d GLY* 4.1 1.3 - - - +
98d ALA* 4.1 20.0 - - + -
99d ILE* 5.0 3.1 - - + +
102d SER* 4.7 6.3 - - - +
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Residues in contact with MET 73 (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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3714 LYS* 5.2 2.9 - - - +
386P LEU* 5.3 0.4 - - - +
63d LEU* 4.7 3.3 - - - +
64d VAL* 3.2 28.3 - - + +
71d ASP* 3.4 11.4 + - - +
72d VAL* 1.3 79.3 - - - +
74d LYS* 1.3 66.9 + - - +
75d LEU* 4.0 32.5 - - + -
92d THR* 4.2 9.0 - - + -
102d SER* 3.5 31.0 - - - +
105d ALA* 4.9 0.7 - - - -
106d THR* 3.5 24.7 - - - +
142d ALA* 3.5 40.4 - - - +
145d ALA* 3.8 9.2 - - + -
146d ILE* 4.1 9.0 - - + -
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Residues in contact with LYS 74 (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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3714 LYS* 5.7 1.6 + - - -
57D SER* 5.1 3.0 + - - +
60D ARG* 4.6 17.2 - - - +
386P LEU* 4.3 27.1 - - + -
61d THR* 4.1 20.3 - - - +
62d GLY 3.6 17.7 + - - +
63d LEU* 4.1 27.8 - - + +
72d VAL 3.4 2.6 + - - +
73d MET* 1.3 83.4 - - - +
75d LEU* 1.4 70.0 + - - +
76d GLN* 4.3 19.7 - - + +
89d ARG* 5.4 1.9 - - - +
90d PHE* 5.3 7.1 - - - +
92d THR* 4.7 11.1 + - - +
145d ALA* 4.7 2.0 - - - -
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Residues in contact with LEU 75 (chain d).
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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3714 LYS* 5.4 4.3 - - - +
62d GLY* 2.9 33.5 + - - +
73d MET* 4.0 19.5 - - + -
74d LYS* 1.4 79.7 - - - +
76d GLN* 1.3 77.5 + - - +
77d ILE* 3.6 24.0 - - + -
88d ALA* 4.6 4.7 - - + -
89d ARG 5.0 4.7 - - - +
90d PHE* 5.5 2.7 - - + -
106d THR* 4.3 22.0 - - + +
109d VAL* 5.6 4.3 - - + -
145d ALA* 4.0 14.0 - - + +
146d ILE* 3.8 39.9 - - + -
149d ALA* 3.9 5.7 - - + +
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Residues in contact with GLN 76 (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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60D ARG* 3.9 20.7 + - - +
59d VAL* 3.7 31.6 - - + +
60d GLY 3.1 13.7 - - - +
61d THR* 3.8 17.5 + - + -
74d LYS* 4.3 14.8 - - + +
75d LEU* 1.3 79.6 - - - +
77d ILE* 1.4 62.6 + - - +
78d GLN 4.3 0.2 - - - -
88d ALA* 3.3 25.1 - - - +
89d ARG* 3.2 59.7 + - + +
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Residues in contact with ILE 77 (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 VAL* 3.5 4.9 - - - +
60d GLY* 3.0 29.3 + - - -
75d LEU* 3.6 28.3 - - + -
76d GLN* 1.4 78.1 - - - +
78d GLN* 1.3 59.3 + - - +
79d VAL* 3.7 23.8 + - + +
85d ILE* 4.2 20.9 - - + -
87d ASP 3.8 4.5 - - - +
88d ALA* 4.8 2.5 - - + -
106d THR* 6.3 0.4 - - + -
109d VAL* 5.9 2.0 - - + -
146d ILE* 5.0 0.7 - - + +
149d ALA* 3.8 31.4 - - + +
150d LEU* 3.6 33.0 - - + -
153d TYR* 4.7 5.6 - - + -
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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