Contacts of the strand formed by residues 49 - 55 (chain B) in PDB entry 1SEJ
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 LYS 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B LYS* 4.1 11.0 - - - +
48B LYS* 1.3 79.9 - - - +
50B ASN* 1.3 69.5 + - - +
69B ASN* 3.4 37.8 - - - +
70B ARG 4.3 2.4 + - - -
71B ILE* 3.9 29.4 - - + -
87B ASN* 3.6 22.8 + - - -
106B SER 2.7 8.6 + - - +
107B ILE* 3.1 9.0 - - + -
108B GLU* 2.8 22.7 + - - -
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Residues in contact with ASN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B THR 3.2 29.5 + - - +
41B ASN* 3.4 11.7 + - - +
42B ASN 3.0 26.1 + - - -
43B LYS* 3.7 7.1 - - - +
49B LYS* 1.3 78.2 - - - +
51B ALA* 1.3 61.9 + - - +
52B LEU* 4.5 1.8 - - + -
69B ASN 4.6 3.4 + - - -
70B ARG* 3.7 7.0 - - + +
71B ILE* 3.1 25.4 + - - +
107B ILE* 5.1 0.7 - - - -
108B GLU* 4.0 2.8 - - - +
109B ASN* 3.0 44.4 + - - +
111B PHE* 3.9 10.3 - - + -
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LYS 4.2 0.2 + - - -
50B ASN* 1.3 73.0 - - - +
52B LEU* 1.3 65.5 + - - +
53B ILE* 3.9 1.1 + - + +
71B ILE* 3.3 12.3 - - + +
73B VAL* 4.3 10.8 - - + -
100B ASN* 4.1 24.5 - - - +
107B ILE* 4.1 19.7 - - + -
109B ASN 3.0 8.4 + - - +
110B ILE* 3.5 5.8 - - + +
111B PHE 2.9 26.7 + - - +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 3.8 5.8 - - + -
40B THR* 3.8 28.9 - - - +
50B ASN 4.5 1.3 - - - -
51B ALA* 1.3 83.7 - - - +
53B ILE* 1.3 63.2 + - - +
54B MET* 3.8 8.2 + - + +
67B LEU* 3.8 27.1 - - + -
70B ARG* 4.0 17.9 - - + -
71B ILE 2.9 12.3 + - - +
72B ILE* 3.5 8.8 - - + +
73B VAL* 2.9 24.5 + - - +
111B PHE* 3.4 29.8 - - + -
113B CYS* 3.4 24.9 - - + -
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ALA 5.0 1.1 - - - +
52B LEU* 1.3 72.1 - - - +
54B MET* 1.3 66.5 + - - +
73B VAL* 3.3 19.3 - - + -
75B ILE* 3.3 26.9 - - + -
94B LEU* 3.8 15.5 - - + -
97B SER* 3.9 6.5 - - - +
98B ILE* 3.8 29.2 - - + -
100B ASN* 4.3 8.7 - - - +
110B ILE* 3.7 26.9 - - + -
111B PHE 2.8 12.4 + - - +
112B VAL* 4.3 9.5 - - + +
113B CYS* 2.6 32.4 + - - +
114B GLY 4.0 0.2 + - - -
118B ILE* 4.3 9.0 - - + -
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Residues in contact with MET 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 5.9 1.1 - - + -
52B LEU* 4.1 16.8 - - + +
53B ILE* 1.3 81.4 - - - +
55B GLY* 1.3 70.0 - - - +
58B THR* 4.0 19.7 - - + -
59B TRP* 3.8 28.5 - - + +
62B ILE* 4.2 11.0 - - + -
67B LEU* 4.6 9.6 - - + -
72B ILE* 3.6 47.3 - - + -
73B VAL 3.0 7.9 + - - +
74B VAL* 3.4 3.3 - - + -
75B ILE* 3.0 22.8 + - - -
113B CYS* 4.3 11.2 - - + -
114B GLY 3.7 8.1 - - - +
118B ILE* 4.2 4.9 - - - -
609B F89 6.3 1.1 - - + -
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Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B MET* 1.3 78.4 - - - +
56B ARG* 1.3 66.5 + - - -
57B LYS 3.3 2.2 - - - -
58B THR* 3.2 2.8 + - - -
59B TRP* 3.0 18.2 + - - +
74B VAL* 4.3 0.2 - - - -
75B ILE 4.0 3.6 - - - -
114B GLY 3.0 13.9 + - - -
118B ILE* 3.5 21.9 - - - +
610B NDP 3.5 18.1 + - - -
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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