Contacts of the strand formed by residues 86 - 91 (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 VAL 86 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37L TYR 3.9 0.2 - - - +
38L GLN* 3.7 1.7 - - - -
39L GLN* 2.8 41.5 + - + +
85L ALA* 1.3 79.6 - - - +
87L TYR* 1.3 67.5 + - - +
88L TYR* 3.5 39.6 + - + +
101L GLN 5.6 0.2 - - - +
102L GLY* 4.6 1.6 - - - -
103L THR 3.6 14.6 - - - +
104L LYS* 4.3 16.6 - - + -
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Residues in contact with TYR 87 (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* 3.1 9.5 + - - -
21L LEU* 3.9 18.6 - - + -
36L TRP* 4.7 4.0 - - + -
37L TYR 3.2 9.2 - - - +
38L GLN* 3.2 34.8 + - + -
48L LEU* 3.6 27.8 - - + -
63L PHE* 4.3 1.2 - + - -
74L LEU* 3.9 12.3 - - + -
76L ILE* 3.7 20.8 - - + +
83L ASP* 2.7 37.7 + - - +
85L ALA 3.9 13.0 - - - -
86L VAL* 1.3 79.1 - - - +
88L TYR* 1.3 61.3 + - - +
102L GLY* 3.3 1.8 - - - -
103L THR* 3.0 29.4 + - - +
105L VAL* 3.9 25.6 - - + -
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Residues in contact with TYR 88 (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* 3.3 18.3 + - - -
43H ARG 3.8 2.6 + - - -
44H GLY* 3.5 27.1 - - - -
45H LEU* 3.7 28.3 - - + -
6L GLN* 3.4 2.0 - - - -
35L ALA 4.0 0.2 - - - +
36L TRP* 3.3 7.0 - - - -
37L TYR* 2.7 46.7 + - + +
39L GLN* 3.4 26.1 + - + -
86L VAL* 3.5 28.5 - - + +
87L TYR* 1.3 75.1 - - - +
89L CYS* 1.3 60.3 + - - +
99L PHE* 4.4 15.5 - - + -
100L GLY 3.4 17.9 - - - -
101L GLN 3.7 14.7 + - - -
102L GLY* 3.7 9.2 - - - -
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Residues in contact with CYS 89 (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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4L LEU* 3.9 13.5 - - - -
6L GLN* 2.8 27.6 + - - +
23L CYS* 2.1 52.5 - - + -
34L LEU* 4.5 3.1 - - + -
35L ALA 3.2 9.2 - - - +
36L TRP* 4.0 15.0 - - + -
88L TYR* 1.3 72.7 - - - +
90L GLN* 1.3 61.6 + - - +
99L PHE* 3.4 8.2 - - - -
100L GLY* 2.9 24.9 + - - -
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Residues in contact with GLN 90 (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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47H TRP* 4.9 0.2 - - - -
113H ALA* 4.9 0.4 - - - +
114H PHE* 3.4 32.0 + - - -
4L LEU* 3.9 3.4 - - - -
34L LEU* 3.1 7.2 - - - +
35L ALA* 2.6 43.1 + - - +
37L TYR* 2.7 35.8 + - + -
89L CYS* 1.3 77.4 - - - +
91L GLN* 1.3 63.3 + - - +
92L TYR* 4.2 16.4 - - - +
97L SER* 3.0 21.7 + - - +
98L THR 3.5 13.7 - - - +
99L PHE* 3.6 26.7 - - + -
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Residues in contact with GLN 91 (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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2L ILE* 3.5 35.0 - - + +
4L LEU* 3.5 15.8 - - + +
29L VAL* 4.1 21.6 - - + +
33L LYS 3.4 8.1 - - - +
34L LEU* 4.4 1.8 - - + +
90L GLN* 1.3 73.7 - - - +
92L TYR* 1.3 57.6 + - - +
93L GLY* 3.4 17.6 + - - -
94L GLN* 3.9 6.3 + - - +
96L LEU 2.8 28.9 + - - -
97L SER* 2.6 28.0 + - - -
98L THR* 2.9 38.2 + - - +
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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