Contacts of the strand formed by residues 92 - 100 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLY 2.8 17.4 + - - +
51A LEU* 3.6 14.9 - - + +
52A VAL 2.9 26.9 + - - +
71A ARG* 4.3 0.7 - - - +
91A CYS* 1.3 75.2 - - - +
93A VAL* 1.3 62.4 + - - +
94A LEU* 4.1 2.2 - - + -
48B THR* 6.0 0.2 - - + -
49B THR 3.2 22.0 - - - +
50B GLY* 3.7 13.4 - - - +
51B LEU* 3.9 14.8 - - + -
96D ALA* 6.1 2.7 - - + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.5 6.5 - - + +
54A VAL* 5.5 0.9 - - + -
66A ILE* 5.3 0.7 - - + -
67A PRO* 3.6 39.4 - - + +
70A VAL* 4.1 27.1 - - + -
71A ARG* 3.7 43.5 - - + +
91A CYS* 3.8 5.1 + - - +
92A ALA* 1.3 76.2 - - - +
94A LEU* 1.3 68.4 + - - +
95A THR* 4.6 5.1 + - - +
95D THR 3.5 9.0 - - - +
96D ALA* 3.7 15.1 - - - +
97D ILE 4.9 0.2 + - - -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.8 21.3 - - + -
52A VAL 2.8 14.6 + - - +
53A PHE* 3.8 15.7 - - + -
54A VAL* 2.8 29.3 + - - +
92A ALA* 4.1 1.8 - - + -
93A VAL* 1.3 74.2 - - - +
95A THR* 1.3 63.9 + - - +
51B LEU* 5.1 4.5 - - + -
94B LEU* 3.6 31.4 - - + -
53C PHE* 4.9 5.8 - - + -
53D PHE* 3.4 22.7 - - + -
94D LEU* 4.4 11.7 - - + -
95D THR 3.3 9.9 - - - +
96D ALA* 3.4 28.7 - - + -
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 4.3 0.2 - - - -
54A VAL* 3.4 3.6 + - - +
66A ILE* 3.9 24.7 - - + +
67A PRO* 4.6 9.6 - - - +
93A VAL* 4.6 2.9 + - - +
94A LEU* 1.3 76.8 + - - +
96A ALA* 1.3 62.4 + - - +
97A ILE* 3.7 31.9 - - + +
67D PRO* 5.9 5.4 - - + +
93D VAL 3.7 1.2 - - - +
94D LEU* 3.5 6.1 - - - -
95D THR* 2.8 56.2 + - + +
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.6 15.3 - - + -
54A VAL 2.8 10.5 + - - +
55A ALA* 3.5 16.5 - - + +
56A GLY 3.5 5.0 + - - +
95A THR* 1.3 73.9 - - - +
97A ILE* 1.3 61.9 + - - +
98A ASP 4.0 0.9 + - - -
48C THR* 4.8 13.8 + - + +
51C LEU* 5.2 0.9 - - + -
67D PRO* 5.9 0.4 - - - -
92D ALA* 6.4 1.3 - - + -
93D VAL 3.7 14.4 - - - +
94D LEU* 3.5 22.2 - - + -
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 5.1 1.1 - - + -
43A ALA* 6.0 1.8 - - + -
54A VAL* 3.6 33.2 - - + +
55A ALA 4.3 7.9 - - - -
56A GLY 3.5 8.1 - - - +
58A ILE* 3.6 38.6 - - + -
66A ILE* 4.1 23.3 - - + -
95A THR* 3.7 25.0 - - + +
96A ALA* 1.3 77.6 - - - +
98A ASP* 1.3 67.8 + - - +
99A GLU* 3.2 16.0 + - + +
65D ASP* 5.2 0.2 - - - +
67D PRO* 3.6 24.4 - - - +
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLY 3.0 14.9 + - - +
57A GLU* 3.7 15.4 - - + +
58A ILE 2.9 25.8 + - - +
96A ALA 4.0 1.4 + - - -
97A ILE* 1.3 70.9 - - - +
99A GLU* 1.3 59.1 + - - +
100A GLN* 2.4 40.9 + - - +
49C THR* 5.8 3.6 - - - +
249C HIS 5.6 1.9 - - - +
67D PRO* 5.6 2.9 - - - -
68D ASN* 5.1 4.0 + - - +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.5 7.8 - - - +
58A ILE* 3.4 35.1 - - + +
60A THR* 4.4 12.6 - - + -
62A GLY 4.3 8.4 - - - +
63A TYR* 5.0 1.6 - - - -
64A VAL* 5.0 8.1 + - - +
66A ILE* 5.6 4.9 - - - +
97A ILE* 3.2 18.0 + - + +
98A ASP* 1.3 72.2 + - - +
100A GLN* 1.3 64.8 + - - +
63D TYR* 3.1 30.3 + - - -
65D ASP* 3.8 21.2 + - - +
67D PRO* 5.6 1.4 - - - +
68D ASN* 3.4 20.7 + - - +
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 5.4 4.2 - - - +
58A ILE 2.9 11.3 + - - +
59A THR* 2.9 17.1 + - - +
60A THR 2.9 23.9 + - - -
98A ASP* 2.4 45.3 + - - +
99A GLU* 1.3 76.1 - - - +
101A SER* 1.3 66.4 + - - +
104A ILE* 4.3 13.9 - - + -
105A ALA* 2.9 32.1 - - + +
68D ASN* 5.2 3.6 - - - +
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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