Contacts of the strand formed by residues 33 - 38 (chain I) in PDB entry 5HHM
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 LEU 33 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5I LEU* 4.8 11.7 - - + -
24I CYS* 4.2 15.9 - - - -
30I PHE* 5.0 9.2 - - + -
32I SER* 1.3 76.4 - - - +
34I GLN* 1.3 76.7 + - - +
35I TRP* 3.7 25.4 - - + +
48I VAL* 4.0 0.9 - - - +
49I THR* 3.2 3.5 - - - -
50I VAL* 2.7 52.3 + - + +
66I PHE* 4.0 16.6 - - + -
71I LYS 6.0 0.9 - - - -
72I ASP* 5.0 2.7 - - - +
73I SER* 3.7 24.2 - - - +
90I CYS* 4.3 4.9 - - + -
91I ALA 3.3 15.9 - - - +
92I GLY* 5.0 0.4 - - - -
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Residues in contact with GLN 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I SER* 4.3 11.0 + - - +
33I LEU* 1.3 82.2 + - - +
35I TRP* 1.3 63.5 + - - +
36I TYR* 3.6 21.5 - - + +
46I LEU* 3.6 15.5 - - + -
48I VAL 3.2 4.9 - - - +
49I THR* 3.0 42.5 + - - +
89I LEU 4.5 0.2 - - - -
90I CYS* 3.2 5.0 - - - -
91I ALA* 2.7 38.6 + - + +
92I GLY* 4.6 1.4 - - - -
93I ALA 4.9 0.2 + - - -
99I LEU* 3.2 27.2 - - - +
100J SER 4.8 0.3 - - - +
101J TYR* 4.3 1.6 - - - -
102J GLU* 3.6 26.5 - - + +
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Residues in contact with TRP 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I GLN* 3.4 23.3 - - - -
22I VAL* 3.8 31.0 - - + -
23I TYR 4.2 2.7 - - - -
24I CYS* 3.6 30.1 - - + -
33I LEU* 3.7 12.0 - - + +
34I GLN* 1.3 70.9 - - - +
36I TYR* 1.3 56.0 + - - +
46I LEU* 3.9 3.6 - - - +
47I LEU* 2.9 35.2 + - + +
48I VAL* 3.3 16.6 + - + +
50I VAL* 5.5 1.6 - - + -
64I PHE* 3.6 36.3 - + + -
73I SER* 2.7 34.5 + - - -
74I SER 3.9 6.5 + - - -
75I LEU* 3.7 26.5 - - + -
88I TYR* 4.5 7.2 - - + -
89I LEU 3.3 13.2 - - - -
90I CYS* 3.8 13.5 - - + -
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Residues in contact with TYR 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I GLN* 3.6 22.5 - - + +
35I TRP* 1.3 76.1 - - - +
37I ARG* 1.3 60.5 + - - +
38I GLN 4.3 0.2 - - - -
44I PRO* 3.8 27.1 - - + -
45I VAL 3.3 6.1 - - - +
46I LEU* 3.6 33.1 - - + +
47I LEU* 3.7 8.0 - - - +
88I TYR* 3.2 5.9 - - - +
89I LEU* 2.8 46.7 + - + +
91I ALA* 4.4 1.6 - - + -
99I LEU* 3.7 7.0 - - + +
101I PHE* 4.2 22.9 - + - -
103J GLN* 2.7 49.8 + - - +
104J TYR* 5.5 0.2 - - - -
105J PHE* 3.5 20.0 - + - -
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Residues in contact with ARG 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I TYR* 1.3 72.6 - - - +
38I GLN* 1.3 65.0 + - - +
39I GLU* 3.4 39.1 + - - +
44I PRO* 4.4 0.7 - - - -
45I VAL* 2.8 41.6 + - + +
47I LEU* 3.8 20.6 - - + +
83I GLY* 3.7 22.7 + - - -
84I ASP* 4.1 2.5 - - - +
85I THR* 2.6 31.1 + - - +
86I GLY* 4.6 0.9 - - - -
87I LEU 3.3 6.3 - - - +
88I TYR* 3.5 37.8 + - + -
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Residues in contact with GLN 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I ARG* 1.3 76.7 - - - +
39I GLU* 1.3 76.7 + - - +
40I PRO* 4.9 2.1 - - - +
41I GLY 5.4 0.4 - - - +
42I GLU 2.9 23.0 + - - +
43I GLY 5.2 0.7 - - - -
44I PRO* 3.7 22.7 - - + +
86I GLY* 3.5 3.8 - - - -
87I LEU* 2.7 58.2 + - + +
89I LEU* 4.5 8.3 - - + +
39J GLN* 2.7 42.6 + - - +
45J LEU* 5.2 0.6 - - - +
90J PHE* 4.1 1.6 - - - -
92J LEU* 3.5 17.2 - - - +
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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