Contacts of the strand formed by residues 42 - 50 (chain A) in PDB entry 1SN8
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 TYR 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ALA 3.7 14.8 + - - -
40A ASN* 3.6 22.3 + - - -
41A ILE* 1.3 93.1 - - - +
43A LYS* 1.3 60.5 + - - +
60A TYR* 3.6 49.6 - + + +
101A ILE* 3.5 8.0 - - - +
102A VAL* 2.9 42.9 + - + -
104A ILE* 3.8 27.6 - - + +
41B ILE* 3.9 10.1 - - - -
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Residues in contact with LYS 43 (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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42A TYR* 1.3 73.3 - - - +
44A GLY* 1.3 58.8 + - - +
45A LYS 4.0 0.5 + - - -
59A ASP 3.9 6.4 - - - +
60A TYR* 4.1 8.3 - - - +
99A GLU* 4.0 26.9 + - + +
100A VAL 3.6 6.3 - - - +
101A ILE* 5.2 0.4 - - + -
39B ALA 5.3 8.1 - - - +
40B ASN* 4.3 26.1 + - - +
41B ILE* 3.9 21.6 - - + +
103B GLN* 4.4 4.9 + - - -
120B ILE* 4.2 6.7 - - - -
121B SER* 2.8 37.8 + - - -
122B LEU* 3.9 17.7 - - + -
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Residues in contact with GLY 44 (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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42A TYR 3.8 2.4 + - - -
43A LYS* 1.3 72.3 - - - +
45A LYS* 1.3 61.8 + - - -
58A VAL* 3.4 23.6 - - - -
59A ASP 3.4 4.7 - - - -
60A TYR* 4.2 5.8 - - - -
98A GLN 3.6 0.3 - - - +
99A GLU* 3.1 6.3 - - - -
100A VAL* 2.8 45.8 + - - +
102A VAL* 4.3 5.3 - - - +
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Residues in contact with LYS 45 (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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43A LYS 4.0 1.0 + - - -
44A GLY* 1.3 72.9 - - - -
46A ILE* 1.3 69.1 + - - +
47A THR* 3.3 6.8 + - + +
58A VAL* 3.4 2.8 - - - -
59A ASP* 2.9 42.7 + - + +
97A GLY* 2.9 40.5 + - - +
98A GLN 3.3 4.7 - - - -
99A GLU* 4.3 20.9 - - + +
123B ALA* 4.1 11.7 - - - +
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Residues in contact with ILE 46 (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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45A LYS* 1.3 72.6 - - - +
47A THR* 1.3 60.0 + - - +
48A ARG 4.5 1.1 - - - +
49A ILE* 3.7 32.1 - - + -
56A ALA* 4.0 11.2 - - + -
57A PHE 3.6 2.2 - - - +
58A VAL* 3.8 23.3 - - + -
68A LEU* 4.4 1.8 - - + -
94A LEU* 3.7 28.7 - - + -
95A ARG 3.4 22.4 - - - +
96A GLU* 3.6 4.4 - - - +
97A GLY* 2.8 27.4 + - - -
98A GLN* 2.8 26.6 + - + +
100A VAL* 4.2 19.3 - - + -
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Residues in contact with THR 47 (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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45A LYS* 3.6 18.4 - - + +
46A ILE* 1.3 74.9 - - - +
48A ARG* 1.3 66.1 + - - +
57A PHE* 2.9 20.7 + - - +
59A ASP* 3.8 15.0 - - + +
65A HIS* 3.3 37.0 + - + -
96A GLU* 3.2 25.8 - - - +
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Residues in contact with ARG 48 (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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46A ILE* 3.9 0.6 - - - +
47A THR* 1.3 87.8 + - - +
49A ILE* 1.3 66.5 + - - +
50A GLU* 3.3 27.7 + - - +
56A ALA* 3.3 3.2 - - - +
57A PHE* 2.8 78.6 + - + +
96A GLU* 4.4 4.9 - - - -
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Residues in contact with ILE 49 (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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46A ILE* 3.7 19.5 - - + -
48A ARG* 1.3 76.3 - - - +
50A GLU* 1.3 70.1 + - - +
51A PRO* 3.4 7.3 - - + +
55A ALA 4.0 3.6 - - - +
56A ALA* 4.3 4.3 - - + -
90A ILE* 3.4 32.1 - - + -
91A LYS* 3.7 29.9 - - + +
94A LEU* 3.5 31.4 - - + +
95A ARG* 3.9 0.9 - - - -
96A GLU* 3.8 27.5 + - + +
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Residues in contact with GLU 50 (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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48A ARG* 3.3 32.1 + - - +
49A ILE* 1.3 74.3 - - - +
51A PRO* 1.3 73.7 - - - +
52A SER* 3.3 9.8 + - - -
53A LEU* 3.1 27.3 + - + +
54A GLU 3.1 17.0 + - - -
55A ALA* 2.9 23.4 + - + +
57A PHE* 4.1 26.9 - - + -
67A PHE* 5.8 0.4 - - + -
90A ILE* 4.2 1.6 - - - -
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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