Contacts of the strand formed by residues 34 - 39 (chain I) in PDB entry 3H3P
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 34 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 4.9 12.6 - - + -
22I CYS* 4.8 12.1 - - - +
24I ALA* 5.5 1.1 - - + -
29I PHE* 4.5 17.9 - - + -
32I TYR 3.5 4.5 + - - +
33I ALA* 1.3 74.9 - - - +
35I SER* 1.3 69.3 + - - +
36I TRP* 4.1 17.5 - - + +
50I GLY* 3.0 2.9 - - - -
51I VAL* 2.7 52.9 + - + +
53I PRO* 5.3 2.7 - - + -
79I ALA* 3.5 35.7 - - + -
96I CYS* 4.6 8.5 - - + -
97I ALA 3.5 9.9 - - - +
98I ARG* 4.5 8.5 - - + +
47T TRP* 4.1 1.1 - - - -
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Residues in contact with SER 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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33I ALA* 5.5 1.1 - - - +
34I LEU* 1.3 77.4 + - - +
36I TRP* 1.3 66.5 + - - +
37I VAL* 4.2 0.9 - - - -
47I TRP* 3.1 26.9 + - - -
49I GLY 3.4 7.3 + - - -
50I GLY* 3.9 4.4 - - - -
96I CYS* 3.1 7.8 - - - +
97I ALA* 2.7 44.9 + - - -
114I PHE* 4.0 26.3 - - - -
47T TRP* 4.4 9.0 - - - -
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Residues in contact with TRP 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 3.8 12.8 - - - -
20I VAL* 3.6 34.5 - - + -
21I SER 4.2 0.7 - - - -
22I CYS* 3.7 31.0 - - + -
34I LEU* 4.1 10.8 - - + +
35I SER* 1.3 75.5 - - - +
37I VAL* 1.3 63.5 + - - +
47I TRP* 4.0 1.2 - - - -
48I MET* 2.8 37.8 + - + +
49I GLY 2.8 14.4 + - - +
50I GLY* 5.2 0.2 - - - -
70I ILE* 3.6 34.8 - - + +
79I ALA* 3.9 10.4 - - + +
80I TYR 4.0 8.5 + - - -
81I LEU* 3.4 48.0 - - + +
94I TYR* 4.1 6.1 - - + -
95I TYR 3.4 18.8 - - - -
96I CYS* 3.8 13.0 - - + -
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Residues in contact with VAL 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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35I SER* 5.1 1.6 - - - -
36I TRP* 1.3 79.7 - - - +
38I ARG* 1.3 63.4 + - - +
45I LEU* 3.8 32.5 - - + -
46I GLU 3.3 13.0 - - - +
47I TRP* 4.2 7.9 - - + -
48I MET* 4.5 1.6 - - - -
94I TYR* 3.6 1.4 - - - -
95I TYR* 2.7 40.8 + - + +
97I ALA* 5.3 2.5 - - + -
114I PHE* 4.2 16.6 - - + -
117I TRP* 4.1 22.2 - - + -
99M PHE* 3.8 24.2 - - + -
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Residues in contact with ARG 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 VAL* 1.3 75.1 - - - +
39I GLN* 1.3 61.8 + - - +
40I ALA* 5.7 1.8 - - - +
44I GLY 3.8 0.7 - - - +
45I LEU* 3.5 4.0 - - - -
46I GLU* 2.8 67.2 + - + +
48I MET* 3.6 22.2 - - + +
63I ARG* 5.1 3.2 - - - +
64I PHE* 3.7 26.2 - - + -
67I ARG* 4.5 3.0 - - - +
89I GLU* 4.2 13.8 + - - +
90I ASP* 3.3 27.0 + - - +
91I THR 5.8 0.2 - - - -
92I ALA* 4.0 9.8 - - - +
93I VAL 3.4 4.9 - - - +
94I TYR* 3.1 41.7 + - + +
95I TYR* 5.3 0.2 - - - -
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Residues in contact with GLN 39 (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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38I ARG* 1.3 76.8 - - - +
40I ALA* 1.3 62.9 + - - +
42I GLY 5.9 0.2 - - - +
43I ARG 3.2 28.2 + - - +
44I GLY 3.8 6.2 - - - +
45I LEU* 3.8 17.5 - - + +
46I GLU* 4.9 0.2 - - - -
92I ALA* 3.3 4.2 - - - -
93I VAL* 2.7 44.9 + - + +
95I TYR* 3.6 17.5 + - + -
39M GLN* 2.9 43.3 + - - -
88M TYR* 3.3 11.9 + - - -
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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