Contacts of the strand formed by residues 43 - 52 (chain H) in PDB entry 1CBV
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 43 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39H GLN* 4.0 13.2 + - - -
40H ALA* 3.0 9.4 + - - +
41H PRO 3.6 1.4 + - - -
42H GLY* 1.3 81.4 - - - +
44H GLY* 1.3 73.7 + - - +
9L LEU* 5.6 3.6 - - - +
92L PHE* 5.7 1.4 - - - -
105L ALA* 3.5 43.0 + - - +
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Residues in contact with GLY 44 (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 ARG 4.0 0.2 - - - +
39H GLN* 3.3 29.4 - - - +
40H ALA 3.9 4.2 + - - -
43H LYS* 1.3 93.1 - - - +
45H LEU* 1.3 67.0 + - - -
46H GLU* 4.0 1.0 + - - +
92L PHE* 5.0 9.2 - - - -
105L ALA* 5.6 3.4 - - - -
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Residues in contact with LEU 45 (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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37H VAL* 4.5 2.5 - - + -
38H ARG 3.7 4.9 - - - +
39H GLN* 3.8 34.1 - - + +
44H GLY* 1.3 73.5 - - - -
46H GLU* 1.3 57.9 + - - +
97H TYR* 4.8 1.8 - - + -
111H TRP* 4.4 20.4 - - + -
41L TYR* 6.1 0.9 - - + -
49L PRO* 4.7 11.2 - - + -
92L PHE* 3.9 35.2 - - + -
103L PHE* 3.3 63.2 + - + +
104L GLY 5.4 1.6 + - - -
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Residues in contact with GLU 46 (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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37H VAL* 3.7 2.9 - - - -
38H ARG* 2.9 71.6 + - + +
44H GLY 4.0 1.1 + - - +
45H LEU* 1.3 74.6 - - - +
47H TRP* 1.3 72.2 + - - +
48H VAL* 3.6 0.7 + - - +
63H ALA* 5.2 1.3 - - + -
65H SER* 2.8 35.4 + - - -
66H VAL* 5.2 0.2 - - - +
101L LEU 5.7 0.7 - - - -
103L PHE* 5.0 1.6 - - - -
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Residues in contact with TRP 47 (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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35H ASN* 3.7 4.0 - - - +
36H TRP 3.9 0.2 - - - -
37H VAL* 3.8 17.3 - - + -
46H GLU* 1.3 80.7 - - - +
48H VAL* 1.3 59.7 + - - +
49H ALA 3.2 28.9 + - - -
50H ARG* 3.6 28.5 - - + +
61H TYR* 3.7 13.2 - - + -
62H TYR* 3.4 24.7 - - - -
63H ALA* 3.1 48.1 - - + +
108H PHE* 3.9 13.0 - + - -
99L VAL* 5.5 9.0 - - + -
100L PRO* 4.0 25.8 - - + -
101L LEU* 3.7 49.7 + - + +
103L PHE* 4.7 2.0 - - - -
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Residues in contact with VAL 48 (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 TRP* 2.9 38.8 + - + +
37H VAL* 3.7 5.4 - - - +
38H ARG* 3.6 37.2 - - + +
46H GLU* 3.6 2.4 + - - +
47H TRP* 1.3 75.5 - - - +
49H ALA* 1.3 66.9 - - + +
62H TYR* 3.4 1.2 - - - -
63H ALA 2.9 25.9 + - - -
66H VAL* 3.2 33.0 - - + +
70H PHE* 3.9 13.0 - - + -
83H LEU* 4.6 3.1 - - + -
96H TYR* 3.9 14.1 - - + -
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Residues in contact with ALA 49 (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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35H ASN* 3.6 0.3 - - - -
36H TRP* 2.8 38.9 + - + +
47H TRP* 3.2 14.9 + - - -
48H VAL* 1.3 87.2 - - + +
50H ARG* 1.3 62.0 + - - +
61H TYR 3.2 6.3 - - - -
62H TYR* 3.3 27.8 - - + -
66H VAL* 5.6 0.4 - - + -
70H PHE* 5.9 1.1 - - + -
72H ILE* 4.3 11.4 - - + -
83H LEU* 4.9 7.0 - - + -
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Residues in contact with ARG 50 (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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1D T 4.0 6.3 - - - -
33H ALA* 3.2 17.3 - - - +
34H MET 3.3 9.4 - - - +
35H ASN* 3.0 42.1 + - - +
47H TRP* 3.6 19.3 - - + +
49H ALA* 1.3 76.2 - - - +
51H ILE* 1.3 69.1 + - - +
52H ARG* 5.0 5.1 - - - +
59H ALA 4.5 0.2 - - - -
60H THR* 3.3 3.6 - - - -
61H TYR* 2.7 57.7 + - + +
72H ILE* 3.6 7.6 - - - +
101H ASP* 2.4 32.3 + - - -
107H TRP* 3.1 41.5 - - - -
108H PHE* 4.0 10.8 - - - -
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Residues in contact with ILE 51 (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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33H ALA* 3.5 4.3 - - - +
34H MET* 2.9 37.8 + - + +
50H ARG* 1.3 78.4 - - - +
52H ARG* 1.3 68.6 + - - +
58H TYR* 3.6 21.8 - - + +
59H ALA 3.3 2.7 - - - -
60H THR* 3.0 20.2 - - - +
72H ILE* 3.6 38.8 - - + +
73H SER* 4.2 1.1 - - - -
74H ARG* 3.3 53.6 - - + +
81H LEU* 5.0 0.4 - - + -
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Residues in contact with ARG 52 (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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1D T 3.1 33.3 + - - +
2D T 3.0 32.0 + - - -
3D T 4.7 5.7 + - - -
33H ALA* 4.3 4.9 - - + -
50H ARG* 5.0 11.2 - - - +
51H ILE* 1.3 80.7 - - - +
53H SER* 1.3 55.9 + - - +
56H ASN* 2.5 42.7 - - + +
58H TYR* 4.2 2.9 - - - -
59H ALA* 2.6 34.8 + - + +
61H TYR* 3.4 34.7 + - + -
74H ARG* 2.8 28.7 + - - -
107H TRP* 5.7 1.6 - - - -
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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