Contacts of the strand formed by residues 52 - 61 (chain B) in PDB entry 1TJJ
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 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B PRO 4.0 1.6 + - - +
51B LEU* 1.3 73.7 - - - +
53B VAL* 1.3 66.9 + - - +
54B ASP* 3.0 28.0 + - - +
78B THR* 4.2 14.9 - - + +
79B PHE 3.4 11.4 - - - +
80B GLU* 3.7 23.8 + - - +
144B VAL 3.5 1.0 - - - +
145B LEU* 3.4 6.4 - - - +
146B SER* 2.7 55.9 + - - +
147B SER* 5.6 0.7 - - - -
148B SER 6.1 0.7 - - - +
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Residues in contact with VAL 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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52B LYS* 1.3 78.2 - - - +
54B ASP* 1.3 61.4 + - - +
55B LEU* 3.8 28.3 - - + -
77B CYS 3.8 0.9 - - - +
78B THR* 3.3 3.3 - - - +
79B PHE* 2.8 51.6 + - + +
82B PHE* 3.6 22.2 - - + -
143B SER* 3.9 5.4 - - - +
144B VAL 3.4 3.8 - - - +
145B LEU* 3.9 16.6 - - + -
2485B LPE 3.4 36.3 - - - +
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Residues in contact with ASP 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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52B LYS* 3.0 33.1 + - - +
53B VAL* 1.3 71.6 - - - +
55B LEU* 1.3 61.3 + - - +
56B VAL* 5.6 1.6 - - + +
77B CYS 3.8 2.2 - - - -
78B THR* 2.5 30.7 + - - +
142B GLU* 3.7 1.7 - - - +
143B SER* 3.5 1.2 - - - -
144B VAL* 2.8 54.4 + - + +
146B SER* 4.7 2.9 + - - -
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Residues in contact with LEU 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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53B VAL* 3.8 12.8 - - + -
54B ASP* 1.3 75.8 - - - +
56B VAL* 1.3 67.1 + - - +
67B LYS* 5.4 0.2 + - - -
73B TYR 5.6 2.5 - - - +
75B GLY 4.2 13.9 - - - +
76B SER* 3.2 22.9 - - - +
77B CYS* 2.8 23.7 + - + +
78B THR* 4.9 1.1 + - - -
79B PHE* 4.0 25.4 - - + -
141B ILE* 4.4 22.0 - - + -
142B GLU 3.3 2.7 - - - +
143B SER* 3.0 37.5 - - - +
2485B LPE 4.5 13.9 - - - -
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Residues in contact with VAL 56 (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 ASP* 5.6 2.2 - - + +
55B LEU* 1.3 78.4 - - - +
57B LEU* 1.3 59.2 - - - +
58B GLU* 4.0 28.0 - - + +
67B LYS* 4.2 33.2 - - + +
76B SER* 3.5 3.1 - - - -
140B ARG 3.7 1.0 - - - +
141B ILE* 3.2 6.0 - - - -
142B GLU* 2.9 57.7 + - + +
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Residues in contact with LEU 57 (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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56B VAL* 1.3 73.5 - - - +
58B GLU* 1.3 62.5 + - - +
67B LYS* 3.6 0.7 - - - -
68B ILE* 2.8 53.5 + - + -
74B ILE* 4.9 1.8 - - + -
75B GLY* 3.7 39.5 - - - +
76B SER* 2.8 10.2 + - - +
139B TYR* 4.5 1.8 - - + -
140B ARG 3.4 6.1 - - - +
141B ILE* 4.1 15.7 - - + -
2484B PFS 3.2 63.0 - - - +
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Residues in contact with GLU 58 (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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56B VAL* 4.0 23.6 - - + +
57B LEU* 1.3 79.3 - - - +
59B LYS* 1.3 62.1 + - - +
65B TRP* 3.9 38.1 - - + +
66B ILE 3.2 10.8 - - - +
67B LYS* 4.0 13.4 + - + +
68B ILE* 4.2 4.9 - - - +
139B TYR* 3.3 8.5 - - - +
140B ARG* 2.9 50.8 + - - +
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Residues in contact with LYS 59 (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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58B GLU* 1.3 75.0 - - - +
60B GLU* 1.3 75.7 + - - +
61B VAL* 3.4 13.7 + - + +
65B TRP* 3.7 3.8 - - - -
66B ILE* 2.9 30.7 + - + +
68B ILE* 4.0 10.3 - - + +
133B TRP 3.8 7.1 + - - -
134B LEU* 2.5 32.0 + - - +
136B THR 2.9 25.3 + - - -
137B GLY* 4.0 9.0 - - - -
138B ASN 3.4 10.3 - - - +
139B TYR* 3.5 31.8 + - + +
2484B PFS 6.3 0.2 - - - -
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Residues in contact with GLU 60 (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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3B SER* 4.4 4.4 + - - -
59B LYS* 1.3 82.6 - - - +
61B VAL* 1.3 64.3 + - - +
62B ALA 4.3 0.2 - - - -
63B GLY* 4.0 27.0 - - - +
64B LEU 3.3 10.3 - - - +
65B TRP* 3.5 35.6 + - + -
138B ASN* 2.7 49.6 + - + +
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Residues in contact with VAL 61 (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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59B LYS* 3.7 21.5 - - + +
60B GLU* 1.3 79.6 - - - +
62B ALA* 1.3 78.8 + - + +
63B GLY 3.1 0.4 - - - -
64B LEU* 2.7 27.2 + - - +
66B ILE* 3.7 25.8 - - + +
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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