Contacts of the strand formed by residues 34 - 40 (chain H) in PDB entry 1KCU
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 ALA 34 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33H TYR* 1.3 73.1 - - - +
35H TRP* 1.3 67.8 + - - +
36H ASN* 3.6 8.7 + - - +
51H TYR* 4.1 31.4 - - + -
52H ILE 3.8 4.7 - - - -
53H SER* 4.1 5.8 - - - +
98H ARG* 3.6 3.6 - - - +
99H GLY 3.0 32.7 + - - +
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Residues in contact with TRP 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H VAL* 4.8 1.8 - - + -
4H LEU* 4.4 9.2 - - + -
24H VAL* 4.0 27.6 - - + -
27H TYR* 3.8 32.1 - + + -
29H ILE* 3.6 40.0 + - + -
32H ASP 3.1 24.6 + - - -
33H TYR* 3.2 11.5 + - + -
34H ALA* 1.3 75.3 - - - +
36H ASN* 1.3 60.6 + - - +
50H ALA 4.1 0.2 - - - +
51H TYR* 3.0 4.6 - - - -
52H ILE* 2.8 51.1 + - + +
53H SER 4.6 0.4 - - - -
54H TYR 4.5 0.9 - - - -
70H ILE* 4.2 1.0 - - - +
79H PHE* 3.6 41.3 - + + -
97H ALA 3.6 3.6 - - - -
98H ARG* 3.7 38.1 - - + -
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Residues in contact with ASN 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ALA* 3.6 11.9 + - - +
35H TRP* 1.3 73.6 - - - +
37H TRP* 1.4 62.9 + - - +
38H ILE* 4.4 7.4 - - + -
48H TRP* 2.8 27.5 + - + +
50H ALA 3.2 4.7 - - - +
51H TYR* 2.8 20.8 - - - +
79H PHE* 3.6 3.1 - - - -
96H CYS* 3.0 9.9 - - - +
97H ALA 2.7 38.9 + - - +
99H GLY* 3.6 20.6 - - - +
103H PHE* 3.3 33.4 - - + -
96L LEU* 5.4 0.9 - - - +
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Residues in contact with TRP 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLN* 4.1 12.3 - - + -
20H LEU* 3.2 45.1 - - + -
21H THR 3.9 6.3 - - - -
22H CYS* 3.4 29.4 - - + -
36H ASN* 1.4 71.1 - - - +
38H ILE* 1.3 64.0 + - - +
48H TRP* 3.9 0.5 - - - -
49H MET* 2.9 42.7 + - + +
50H ALA 2.8 12.3 + - - +
70H ILE* 3.7 20.4 - - + -
79H PHE* 3.1 32.7 - + - -
80H PHE 3.8 0.6 - - - -
81H LEU* 3.5 41.3 - - + +
94H TYR* 4.5 12.8 - - + -
95H TYR 3.2 32.5 - - - -
96H CYS* 4.0 8.1 - - + -
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Residues in contact with ILE 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H ASN* 4.4 3.4 - - + -
37H TRP* 1.3 80.7 - - - +
39H ARG* 1.3 62.2 + - - +
46H LEU* 4.5 6.7 - - + -
47H GLU 3.2 27.1 - - - +
48H TRP* 3.9 15.0 - - + +
49H MET* 4.4 3.3 - - - +
94H TYR* 3.6 0.9 - - - +
95H TYR* 2.6 44.3 + - + +
97H ALA* 4.3 11.2 - - + -
103H PHE* 3.7 45.8 - - + -
106H TRP* 3.9 28.5 - - + -
98L PHE* 4.4 9.4 - - + -
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Residues in contact with ARG 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ILE* 1.3 76.6 - - - +
40H GLN* 1.3 60.5 + - - +
41H PHE* 3.2 27.5 - - + -
45H LYS 3.8 0.9 - - - +
46H LEU* 3.6 3.1 - - - +
47H GLU* 2.8 67.9 + - - +
49H MET* 3.7 20.1 - - - -
64H LEU* 3.5 22.9 - - - +
67H ARG* 5.2 2.8 - - - +
83H LEU* 5.4 3.2 - - - +
89H GLU 5.3 0.2 + - - -
90H ASP* 3.2 35.0 + - - +
92H ALA* 4.8 3.4 - - + -
93H ILE 3.2 10.5 - - - +
94H TYR* 3.3 41.1 + - + -
95H TYR* 5.0 0.9 - - - -
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Residues in contact with GLN 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ARG* 1.3 76.0 - - - +
41H PHE* 1.3 63.6 + - - +
44H ASN* 3.0 34.2 + - - +
45H LYS 3.3 11.9 - - - +
46H LEU* 3.3 20.7 - - + +
92H ALA* 2.9 20.7 - - - +
93H ILE* 2.7 35.6 + - + +
95H TYR* 3.6 22.6 + - + -
38L GLN* 2.9 43.1 - - - +
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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