Contacts of the strand formed by residues 44 - 51 (chain H) in PDB entry 5U2V
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 ARG 44 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H TYR* 3.2 7.5 - - - -
36H ARG* 2.9 53.7 + - + +
38H ASP* 2.7 30.9 + - - +
41H MET* 3.5 31.2 - - + +
42H GLY 3.4 13.1 + - - +
43H LEU* 1.3 74.0 - - - +
45H LEU* 1.3 63.6 - - - +
46H ILE* 3.5 2.4 + - - +
59H GLU* 3.7 30.5 - - - +
60H VAL* 3.8 32.6 - - + +
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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
----------------------------------------------------------
61A ARG* 6.3 0.2 - - - +
96G GLN* 5.6 12.3 - - + +
33H TYR* 3.9 21.5 - - + -
34H TRP 3.5 15.9 - - - +
35H TYR* 3.5 33.3 - - + +
43H LEU 4.2 0.2 + - - -
44H ARG* 1.3 71.5 - - - +
46H ILE* 1.3 58.2 + - - +
47H TYR 3.5 14.6 - - - +
48H TYR* 3.9 26.5 - - + -
58H GLY* 4.0 11.2 - - - -
59H GLU* 2.6 39.2 + - + +
60H VAL* 3.1 7.5 + - - +
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Residues in contact with ILE 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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34H TRP* 2.7 20.8 + - + +
35H TYR 3.6 23.8 - - - +
36H ARG* 3.6 7.9 - - + +
44H ARG 3.9 7.0 - - - +
45H LEU* 1.3 73.9 - - - +
47H TYR* 1.3 73.7 + - + +
58H GLY* 2.8 24.4 + - - -
60H VAL* 3.6 18.8 - - + +
61H PRO* 3.7 9.5 - - - +
64H TYR* 3.6 37.5 - - + -
76H LEU* 4.2 13.2 - - + -
89H TYR* 3.7 29.4 - - + -
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Residues in contact with TYR 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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34H TRP* 3.1 26.4 + - - +
45H LEU* 3.5 7.4 - - - +
46H ILE* 1.3 91.9 - - + +
48H TYR* 1.3 62.2 + - - +
55H THR* 5.2 2.0 - - - -
56H ASP* 3.4 24.2 - - - -
57H LYS* 3.6 15.6 - - + +
58H GLY 3.7 1.6 - - - +
61H PRO* 3.5 30.9 + - + +
64H TYR* 3.3 30.7 + - + -
65H ASN* 3.8 8.8 - - + +
66H VAL* 3.4 46.9 - - + -
74H PHE* 4.0 2.1 - - - -
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Residues in contact with TYR 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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61A ARG* 2.9 40.9 + - - -
64A GLN* 3.5 25.3 - - + +
96G GLN* 4.8 7.1 + - - -
32H MET 3.5 13.2 - - - +
33H TYR* 3.9 23.6 - + + -
45H LEU* 3.9 20.0 - - + -
47H TYR* 1.3 75.0 - - - +
49H SER* 1.3 64.0 + - - +
50H ALA* 3.9 25.4 - - + -
55H THR* 3.3 5.5 - - - -
56H ASP* 2.9 55.7 + - + -
57H LYS 3.6 20.6 - - - -
58H GLY* 4.9 0.2 - - - -
74H PHE* 3.6 5.3 - - - -
97H THR* 5.2 3.8 - - + -
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Residues in contact with SER 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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30H ASN 3.8 0.7 - - - +
31H SER* 3.2 3.2 - - - -
32H MET 2.9 33.0 + - - +
48H TYR* 1.3 77.7 - - - +
50H ALA* 1.3 63.8 + - - +
51H SER 3.3 3.8 + - - -
54H THR 2.6 23.8 + - - -
55H THR* 4.1 0.7 - - - +
68H ARG* 2.9 30.3 + - - +
74H PHE* 3.6 25.6 - - - -
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Residues in contact with ALA 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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64A GLN* 3.5 31.1 + - + +
65A LEU* 5.1 1.3 - - - -
68A GLY* 4.7 6.7 - - - -
30H ASN* 3.4 5.9 - - - +
31H SER* 2.8 18.9 + - - -
48H TYR* 3.9 20.3 - - + -
49H SER* 1.3 72.3 - - - +
51H SER* 1.3 62.9 + - - +
54H THR* 3.9 11.6 + - + +
96H TRP* 5.2 1.4 - - - -
97H THR* 3.8 25.1 + - + +
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Residues in contact with SER 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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67A ARG* 3.8 6.4 + - - +
68A GLY* 3.5 27.2 + - - -
71A GLN* 4.2 14.9 - - - +
30H ASN* 3.1 24.7 - - - -
49H SER* 3.2 6.6 + - - -
50H ALA* 1.3 80.3 - - - +
52H GLU* 1.3 74.8 + - - +
53H GLY 3.1 2.8 + - - -
54H THR* 3.3 24.3 + - - +
68H ARG* 4.2 0.7 - - - -
96H TRP* 5.1 0.4 - - - -
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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