Contacts of the strand formed by residues 34 - 39 (chain A) in PDB entry 4KZK
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 LYS 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 1.3 74.7 - - - +
35A ILE* 1.3 65.1 + - - +
64A THR* 3.3 32.5 - - + +
66A VAL* 3.8 24.0 - - + -
86A GLN* 2.8 44.6 + - + +
87A LYS* 4.2 3.3 - - - +
88A ALA* 3.4 16.7 - - + +
89A GLN* 2.8 36.6 + - - +
90A GLY 3.6 2.9 + - - -
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Residues in contact with ILE 35 (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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33A VAL* 4.4 4.5 - - + -
34A LYS* 1.3 77.7 - - - +
36A GLY* 1.3 74.3 + - - +
63A PHE* 3.9 36.6 - - + -
64A THR 2.9 6.1 + - - -
65A LEU* 3.5 11.7 - - + +
66A VAL* 3.0 26.2 + - - -
88A ALA* 4.9 1.1 - - - -
90A GLY 3.4 7.6 - - - +
92A ILE* 4.3 13.9 - - + -
295A SER* 3.9 7.6 - - - +
298A MET* 3.7 27.4 - - + -
299A TYR* 3.8 21.3 - - + +
302A ILE* 3.8 17.5 - - + -
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Residues in contact with GLY 36 (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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35A ILE* 1.3 80.4 - - - +
37A PHE* 1.3 59.6 + - - +
38A VAL 4.1 1.1 - - - -
66A VAL 3.4 9.0 - - - -
83A LEU* 3.7 28.5 - - - +
88A ALA* 4.6 0.4 - - - +
90A GLY 2.8 14.1 + - - -
91A VAL* 3.3 3.5 - - - -
92A ILE* 2.9 25.1 + - - +
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Residues in contact with PHE 37 (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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35A ILE* 5.7 0.2 - - + -
36A GLY* 1.3 70.7 - - - -
38A VAL* 1.3 63.6 + - - +
39A VAL* 3.9 9.6 - - + -
50A GLU* 3.4 34.5 - - + -
51A TRP* 3.0 39.7 + + + +
54A ALA* 3.8 17.5 - - + -
65A LEU* 4.0 14.6 - - + -
66A VAL 2.9 10.5 + - - +
67A LYS* 3.6 0.9 - - - -
68A ILE 3.2 13.9 + - - +
92A ILE* 3.3 27.6 - - + -
118A VAL* 4.1 11.2 - - + -
290A HIS 3.6 17.7 - - - -
291A GLY* 4.0 6.1 - - - -
294A THR* 3.8 17.3 - - - -
295A SER* 3.9 13.7 - - - -
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Residues in contact with VAL 38 (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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37A PHE* 1.3 77.7 - - - +
39A VAL* 1.3 66.4 + - - +
68A ILE* 3.2 19.3 - - + +
70A ALA* 3.7 27.4 - - + -
76A VAL* 5.2 0.2 - - + -
79A ALA* 4.3 12.6 - - + -
80A LEU* 5.2 1.3 - - + -
83A LEU* 4.0 16.6 - - + -
91A VAL* 3.9 20.2 - - + -
92A ILE 2.8 7.4 + - - +
93A ILE* 3.3 30.7 - - + +
94A CYS 2.9 25.3 + - - +
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Residues in contact with VAL 39 (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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37A PHE* 3.9 16.2 - - + -
38A VAL* 1.3 80.2 - - - +
40A LYS* 1.3 63.8 + - - +
41A GLN 4.3 4.7 - - - +
42A PRO* 4.3 8.7 - - + -
47A PHE* 3.6 44.6 - - + +
50A GLU* 4.2 0.4 - - - +
51A TRP* 3.5 45.3 - - + +
68A ILE 3.0 8.2 + - - +
69A ALA* 3.6 2.8 - - - -
70A ALA* 2.9 24.8 + - - -
94A CYS* 3.7 4.9 - - + -
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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