Contacts of the strand formed by residues 34 - 39 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L LEU* 4.4 11.4 - - + -
23L CYS* 4.0 18.8 - - - -
29L VAL* 4.4 6.5 - - + -
32L ASN 2.9 7.3 + - - +
33L LYS* 1.3 74.4 - - - +
35L ALA* 1.3 64.9 + - - +
36L TRP* 3.8 21.8 - - + +
49L ILE* 4.3 0.9 - - - +
50L TYR* 3.9 0.5 - - - -
51L GLY 3.5 3.5 + - - -
52L ALA* 2.8 34.6 + - - +
72L PHE* 3.1 68.0 - - + -
89L CYS* 4.9 0.2 - - + -
90L GLN 3.1 23.1 - - - +
91L GLN 4.4 0.9 - - - +
92L TYR* 3.7 2.8 - - - -
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Residues in contact with ALA 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H ALA* 3.8 27.1 - - + -
34L LEU* 1.3 75.7 - - - +
36L TRP* 1.3 65.8 + - - +
37L TYR* 3.9 12.8 - - + -
47L LEU* 3.9 8.1 - - + -
49L ILE 3.1 14.6 - - - +
50L TYR* 4.2 0.7 - - - -
88L TYR 4.0 0.2 - - - +
89L CYS* 3.2 6.6 - - - +
90L GLN* 2.6 41.2 + - - +
92L TYR* 3.7 6.2 - - + -
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Residues in contact with TRP 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLN* 4.1 16.6 - - - -
21L LEU* 3.8 25.4 - - + -
22L SER 4.1 6.3 - - - -
23L CYS* 3.6 31.6 - - + -
34L LEU* 3.8 17.6 - - + +
35L ALA* 1.3 76.7 - - - +
37L TYR* 1.3 67.3 + - - +
47L LEU* 3.6 3.6 - - - +
48L LEU* 3.1 26.1 + - + -
49L ILE* 2.9 38.8 + - + +
52L ALA 4.8 3.7 + - - -
65L GLY* 5.2 0.4 - - - -
66L SER 5.5 0.2 + - - -
72L PHE* 4.2 4.5 - - + +
73L THR* 4.0 11.5 + - - -
74L LEU* 3.4 57.8 - - + +
87L TYR* 4.7 4.9 - - + -
88L TYR 3.3 18.4 - - - -
89L CYS* 4.0 12.8 - - + -
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Residues in contact with TYR 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H LEU* 5.4 0.7 - - + -
113H ALA* 3.8 1.6 - - - +
114H PHE* 2.8 52.4 + + + +
117H TRP* 4.0 20.4 - + - -
35L ALA* 3.9 7.6 - - + -
36L TRP* 1.3 76.5 - - - +
38L GLN* 1.3 60.0 + - - +
45L PRO* 4.2 13.0 - - + -
46L ARG 3.3 19.5 - - - +
47L LEU* 3.5 18.3 - - + +
48L LEU* 4.1 5.6 - - - -
86L VAL 3.9 0.2 - - - +
87L TYR* 3.2 8.7 - - - +
88L TYR* 2.7 47.5 + - + +
90L GLN* 2.7 39.3 + - + -
99L PHE* 4.0 16.4 - + - -
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Residues in contact with GLN 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L TYR* 1.3 73.6 - - - +
39L GLN* 1.3 63.5 + - - +
40L ARG* 3.1 37.6 + - - +
44L ALA 4.4 0.5 - - - +
45L PRO* 3.2 2.1 - - - +
46L ARG* 2.7 66.3 + - + +
48L LEU* 3.8 16.5 - - + +
63L PHE* 3.8 18.2 - - - -
82L GLU 4.3 3.4 + - - -
83L ASP* 4.1 7.7 + - - -
85L ALA* 3.9 10.3 - - + -
86L VAL 3.7 2.9 - - - -
87L TYR* 3.2 34.2 + - + -
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Residues in contact with GLN 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLN* 3.0 40.6 + - - -
45H LEU* 4.6 0.7 - - - +
95H TYR* 3.5 10.1 + - - -
38L GLN* 1.3 75.3 - - - +
40L ARG* 1.3 64.4 + - - +
41L PRO* 4.6 1.0 - - - +
42L GLY 5.9 0.8 - - - +
43L GLN 2.9 29.0 + - - +
44L ALA 4.1 1.1 - - - -
45L PRO* 3.9 27.8 - - + +
85L ALA* 3.2 4.6 - - - +
86L VAL* 2.8 44.9 + - + +
88L TYR* 3.4 19.8 + - + -
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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