Contacts of the strand formed by residues 92 - 100 (chain A) in PDB entry 3IML
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 3.0 14.0 + - - +
51A LEU* 3.3 10.6 - - + +
52A VAL 2.9 23.9 + - - +
90A GLY 3.7 1.8 - - - -
91A CYS* 1.3 75.2 - - - +
93A VAL* 1.3 61.0 + - - +
94C LEU* 4.0 12.8 - - + -
95C VAL 3.2 7.2 - - - +
96C ALA* 3.6 28.0 - - + +
51D LEU* 4.8 9.0 - - + -
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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* 3.3 26.2 - - + +
54A LEU* 4.1 23.3 - - + -
67A ILE* 3.8 45.5 - - + +
70A ALA* 5.3 4.9 - - + -
71A ARG* 4.4 8.7 - - + +
91A CYS* 3.8 12.3 - - - +
92A ALA* 1.3 79.9 - - - +
94A LEU* 1.3 59.7 + - - +
95A VAL* 4.0 4.0 + - + -
93C VAL 3.6 2.1 - - - +
94C LEU* 3.4 3.7 - - - +
95C VAL* 2.8 41.8 + - - +
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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* 4.8 3.3 - - + +
52A VAL 2.8 12.7 + - - +
53A VAL* 3.5 16.0 - - + +
54A LEU* 2.9 30.3 + - - +
92A ALA 4.3 0.2 - - - -
93A VAL* 1.3 71.6 - - - +
95A VAL* 1.3 62.2 + - - +
96A ALA* 4.8 3.4 - - + -
51B LEU* 3.6 36.6 - - + -
53B VAL* 4.7 0.4 - - + -
94B LEU* 4.1 23.3 - - + -
51C LEU* 4.3 8.5 - - + -
92C ALA* 4.3 16.4 - - + -
93C VAL 3.5 10.5 - - - +
94C LEU* 3.8 32.9 - - + +
94D LEU* 5.4 4.5 - - + -
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Residues in contact with VAL 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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54A LEU* 3.7 12.1 - - + -
66A TYR* 4.2 13.5 - - + -
67A ILE* 4.0 20.9 - - + -
93A VAL* 4.1 7.2 - - + -
94A LEU* 1.3 73.2 - - - +
96A ALA* 1.3 57.8 + - - +
97A TYR* 3.7 34.5 - - + +
67C ILE* 3.5 33.7 - - + -
71C ARG* 5.0 8.9 + - - +
91C CYS 4.2 2.3 - - - +
92C ALA* 3.4 2.5 - - - -
93C VAL* 2.8 37.2 + - + +
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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 VAL* 5.5 0.7 - - + -
54A LEU 2.8 16.2 + - - +
55A ALA* 4.0 7.8 - - + -
56A GLY 4.3 0.9 + - - -
94A LEU* 4.8 3.6 - - + -
95A VAL* 1.3 73.8 - - - +
97A TYR* 1.3 67.0 + - - +
98A ASP 3.6 1.0 + - - -
48B ASN* 3.2 31.2 + - - +
51B LEU* 3.9 19.1 - - + -
91C CYS 5.4 0.9 - - - -
92C ALA* 3.9 23.1 - - + +
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Residues in contact with TYR 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* 3.2 32.5 - - + +
43A ALA* 4.0 15.6 - - + +
44A GLU 4.6 0.7 + - - -
45A THR* 5.3 0.9 + - - -
54A LEU* 3.6 22.0 - - + +
55A ALA* 3.3 35.0 - - - -
56A GLY 3.3 8.7 - - - +
58A ILE* 3.6 29.8 - - + -
66A TYR* 3.7 36.6 - + + -
95A VAL* 3.6 22.2 - - + +
96A ALA* 1.3 79.1 - - - +
98A ASP* 1.3 63.3 + - - +
99A LYS* 3.4 12.9 + - + +
71C ARG* 5.7 1.4 + - - -
90C GLY 4.7 16.1 + - - +
91C CYS 5.5 1.2 - - - +
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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 2.7 13.4 + - - +
57A GLU* 3.5 20.4 - - - +
58A ILE 3.0 24.1 + - - -
96A ALA 3.6 2.2 + - - -
97A TYR* 1.3 68.9 - - - +
99A LYS* 1.3 59.9 + - - +
100A GLN* 3.0 30.6 + - - +
48B ASN* 6.2 1.8 - - - +
49B THR* 5.2 12.8 - - + +
240B GLN 5.6 0.9 - - - +
241B GLY 5.2 5.4 - - - +
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Residues in contact with LYS 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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58A ILE* 3.3 16.8 - - + +
60A THR* 4.6 10.1 - - + -
62A ALA 4.3 18.8 + - - -
63A ASN* 4.8 10.9 + - - +
64A ILE 5.5 1.4 + - - +
66A TYR* 3.5 35.0 + - + +
97A TYR* 3.4 16.0 + - + +
98A ASP* 1.3 77.4 + - - +
100A GLN* 1.3 74.4 + - - +
68C GLN* 5.1 9.7 - - - +
71C ARG* 4.9 14.2 - - - +
90C GLY 5.3 13.0 + - - +
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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* 5.3 2.4 - - - +
58A ILE 3.1 9.1 + - - +
59A THR* 3.2 27.1 + - + +
60A THR 3.1 26.3 + - - +
98A ASP* 3.0 41.1 + - - +
99A LYS* 1.3 80.8 + - - +
101A SER* 1.3 70.2 + - - +
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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