Contacts of the strand formed by residues 54 - 60 (chain B) in PDB entry 2Y1T
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 54 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.8 23.5 - - - -
50B LEU* 4.5 4.0 - - + +
51B PRO* 3.2 29.5 + - + +
52B GLU 3.4 15.9 - - - -
53B GLY* 1.3 82.0 - - - +
55B GLU* 1.3 62.5 + - - +
81B GLU* 3.3 26.7 + - - +
113B ILE* 3.8 27.4 - - + -
114B MET* 3.3 25.1 - - - -
115B LYS* 3.5 39.1 - - + +
116B LYS* 3.6 6.0 - - - +
118C PRO* 4.2 18.9 - - + +
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Residues in contact with GLU 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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21A GLY 4.4 2.8 - - - +
22A ASP* 5.6 0.3 - - - -
23A TRP* 3.0 33.6 + - - -
112A ARG* 3.0 24.7 + - - +
50B LEU* 4.0 5.6 - - - -
54B TYR* 1.3 74.3 - - - +
56B ALA* 1.3 58.5 + - - +
57B HIS* 2.6 32.2 + - + +
78B VAL* 4.1 4.6 - - + +
79B ILE 3.2 17.0 - - - +
80B ASP* 4.4 7.5 - - - +
113B ILE* 3.3 5.5 - - - +
114B MET 2.9 38.8 + - - +
116B LYS* 3.8 18.4 - - + +
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Residues in contact with ALA 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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50B LEU* 3.5 13.8 - - + +
55B GLU* 1.3 71.8 - - - +
57B HIS* 1.3 72.4 + - - +
77B GLY 3.6 0.3 - - - +
78B VAL* 3.4 1.4 - - - +
79B ILE* 2.7 41.4 + - + -
90B TRP* 3.5 32.3 - - + -
111B PHE* 4.0 8.5 - - + -
112B ARG 3.1 11.2 - - - +
113B ILE* 4.3 1.1 - - + +
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Residues in contact with HIS 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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23A TRP* 4.3 10.6 - + - -
112A ARG* 4.9 0.7 - - - -
114A MET* 5.0 4.9 - - + -
23B TRP* 3.5 16.8 - - + -
55B GLU* 2.6 34.9 + - + +
56B ALA* 1.3 83.3 - - - +
58B VAL* 1.3 61.7 + - - +
76B MET* 3.9 27.7 - - + -
77B GLY 3.2 3.1 - - - -
78B VAL* 4.5 12.1 - - + -
111B PHE* 3.1 25.3 - - - +
112B ARG* 2.9 13.8 + - + +
114B MET* 3.3 45.0 - - + +
76C MET* 5.9 1.6 - - - +
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Residues in contact with VAL 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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26B LEU* 5.2 1.1 - - + -
44B LEU* 5.2 4.7 - - + -
57B HIS* 1.3 74.9 - - - +
59B VAL* 1.3 63.6 + - - +
72B GLN* 3.1 14.3 + - - +
76B MET* 3.2 6.3 - - - +
77B GLY* 2.8 47.3 + - - +
79B ILE* 4.1 15.5 - - + -
90B TRP* 3.9 31.4 - - + -
91B PHE 5.4 3.6 - - - +
92B PHE* 4.9 2.9 - - + -
109B CYS* 3.8 31.9 - - + -
110B GLN 3.3 6.7 - - - +
111B PHE* 4.1 3.8 - - + -
143B DUD 4.9 6.5 - - + +
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Residues in contact with VAL 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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23B TRP* 3.7 26.5 - - + -
57B HIS 4.2 0.4 - - - -
58B VAL* 1.3 79.2 - - - +
60B PRO* 1.3 83.8 - - + +
72B GLN* 3.3 5.2 - - - -
75B SER 4.2 3.1 - - - +
76B MET* 3.6 37.2 - - + -
109B CYS* 3.2 3.3 - - - +
110B GLN* 2.9 43.0 + - + +
74C ASN 4.4 0.4 - - - +
76C MET* 4.1 24.9 - - + +
78C VAL* 4.7 1.3 - - + -
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Residues in contact with PRO 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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59B VAL* 1.3 103.4 - - + +
61B ARG* 1.3 71.6 + - - +
62B SER 3.8 0.7 + - - -
64B THR* 4.2 13.5 - - + -
70B VAL 5.8 0.9 - - - +
71B ILE* 5.5 0.7 - - - -
72B GLN* 3.1 31.2 - - + +
92B PHE* 4.1 8.3 - - + -
108B ILE 4.0 6.1 - - - +
109B CYS* 4.0 1.8 - - + -
110B GLN* 3.8 4.6 - - - +
73C THR 4.4 5.4 - - - +
74C ASN* 3.3 32.0 + - - +
75C SER* 3.6 13.2 - - - +
76C MET 5.0 1.4 - - - +
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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