Contacts of the strand formed by residues 92 - 100 (chain C) in PDB entry 5H9U
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 ALA 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C GLY 2.6 17.4 + - - +
51C LEU* 3.3 15.1 - - + +
52C VAL 2.8 26.9 + - - -
71C ARG* 4.5 0.9 - - - +
91C CYS* 1.3 74.5 - - - +
93C VAL* 1.3 63.6 + - - +
94C LEU* 4.1 1.6 - - + -
48D THR* 5.9 0.2 - - + -
49D THR 3.2 22.0 - - - +
50D GLY* 3.7 13.0 - - - +
51D LEU* 3.8 15.5 - - + -
92D ALA* 4.6 0.7 - - + -
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR 3.7 8.3 - - - +
96B ALA* 3.9 13.6 - - - +
52C VAL* 3.4 7.2 - - + +
54C VAL* 5.2 1.1 - - + -
66C ILE* 5.0 1.3 - - + -
67C PRO* 3.8 38.3 - - + +
70C VAL* 3.8 36.3 - - + -
71C ARG* 3.8 36.4 - - + +
91C CYS* 3.8 6.2 + - - -
92C ALA* 1.3 77.4 - - - +
94C LEU* 1.3 67.8 + - - +
95C THR* 4.8 3.9 + - - +
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 3.6 20.0 - - + -
94B LEU* 4.5 8.7 - - + -
95B THR 3.6 8.3 - - - +
96B ALA* 3.5 28.7 - - + -
51C LEU* 3.7 17.3 - - + -
52C VAL 2.7 13.0 + - - +
53C PHE* 3.7 31.6 - - + -
54C VAL* 2.8 33.8 + - - +
92C ALA* 4.1 0.9 - - + -
93C VAL* 1.3 74.2 - - - +
95C THR* 1.3 59.5 + - - +
51D LEU* 4.5 5.8 - - + -
94D LEU* 3.5 32.8 - - + -
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Residues in contact with THR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PRO* 6.2 3.1 - - + -
93B VAL 3.6 1.7 - - - +
94B LEU* 3.5 7.3 - - - +
95B THR* 3.0 49.0 + - + -
54C VAL* 3.5 3.6 - - - +
66C ILE* 3.9 25.1 - - + +
67C PRO* 4.8 9.8 - - - +
93C VAL* 4.8 2.3 + - - +
94C LEU* 1.3 77.1 + - - +
96C ALA* 1.3 62.4 + - - +
97C ILE* 3.8 31.2 - - + +
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 4.7 10.1 + - + +
51A LEU* 4.8 6.5 - - + -
92B ALA* 6.1 2.2 - - + -
93B VAL 3.8 13.9 - - - +
94B LEU* 3.5 21.5 - - + -
53C PHE* 4.0 16.2 - - + -
54C VAL 2.8 12.0 + - - +
55C ALA* 3.6 14.9 - - + +
56C GLY 3.7 4.3 + - - +
95C THR* 1.3 72.6 - - - +
97C ILE* 1.3 61.6 + - - +
98C ASP 4.0 1.0 + - - -
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Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PRO* 4.3 19.8 - - - +
93B VAL 5.1 0.2 + - - -
28C ILE* 5.2 0.4 - - + -
43C ALA* 6.0 1.3 - - + -
54C VAL* 3.7 35.0 - - + +
55C ALA 4.2 7.4 - - - +
56C GLY 3.6 11.0 - - - +
58C ILE* 3.7 43.5 - - + -
66C ILE* 4.3 17.3 - - + -
95C THR* 3.8 23.5 - - + +
96C ALA* 1.3 78.5 - - - +
98C ASP* 1.3 68.7 + - - +
99C GLU* 3.2 12.9 + - + +
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Residues in contact with ASP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 5.5 7.4 - - - +
249A HIS 5.7 1.0 - - - +
67B PRO* 6.2 0.9 - - - -
56C GLY 3.0 13.8 + - - +
57C GLU* 3.5 15.4 - - + +
58C ILE 3.0 21.7 + - - -
96C ALA 4.0 1.6 + - - -
97C ILE* 1.3 70.5 - - - +
99C GLU* 1.3 68.1 + - - +
100C GLN* 3.7 11.8 + - - +
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Residues in contact with GLU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TYR* 4.2 26.1 + - - -
65B ASP* 4.5 22.7 + - - +
67B PRO* 6.2 1.2 - - - +
32C LEU* 5.4 2.3 - - - +
58C ILE* 3.1 26.7 - - + +
60C THR* 4.1 20.3 - - + +
62C GLY 4.2 6.5 - - - +
63C TYR* 4.6 9.1 - - - -
64C VAL 5.8 0.2 + - - -
97C ILE* 3.2 13.4 + - + +
98C ASP* 1.3 79.5 + - - +
100C GLN* 1.3 67.8 + - - +
101C SER 4.0 1.7 + - - +
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Residues in contact with GLN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ARG* 4.7 4.1 + - - +
57C GLU* 3.0 38.0 - - - +
58C ILE 2.3 33.7 + - - +
59C THR* 2.1 37.9 + - + +
60C THR 2.8 34.0 + - - +
98C ASP* 3.7 14.2 + - - +
99C GLU* 1.3 72.7 - - - +
101C SER* 1.3 58.8 + - - +
104C ILE* 5.6 5.6 - - + -
105C ALA* 4.7 17.4 - - + +
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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