Contacts of the strand formed by residues 47 - 54 (chain B) in PDB entry 1YA8
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 VAL 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.5 3.0 - - - -
38B VAL* 2.7 38.1 + - - +
40B LEU* 5.6 2.5 - - + +
45B GLN 4.5 4.7 - - - +
46B PRO* 1.3 72.1 - - - +
48B ALA* 1.3 67.2 + - - +
49B ILE* 3.6 12.0 + - + +
122B TYR* 4.1 6.7 - - + -
123B THR 3.0 29.4 - - - +
124B PRO* 4.1 13.0 - - + -
155B LEU* 3.8 27.4 - - + +
158B ALA* 4.4 6.1 - - + -
159B ALA* 4.1 24.0 - - + +
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PRO* 4.0 4.7 - - + -
36B LYS 3.8 4.7 - - - -
37B PHE* 3.8 16.6 - - + -
46B PRO 3.7 2.8 + - - -
47B VAL* 1.3 71.9 - - - +
49B ILE* 1.3 59.6 + - - +
50B PHE* 3.9 9.0 - - + -
121B ILE 3.8 1.0 - - - +
122B TYR* 3.7 1.6 - - - -
123B THR* 2.8 56.4 + - + +
125B ALA 5.3 1.8 - - - +
127B LEU* 3.7 21.3 - - + -
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY* 3.3 8.0 - - - -
36B LYS* 3.0 43.5 + - + +
38B VAL* 3.6 34.1 - - + -
47B VAL* 3.9 11.7 - - + +
48B ALA* 1.3 76.8 - - - +
50B PHE* 1.3 68.9 + - - +
51B LEU* 4.0 24.7 - - + -
80B ALA 4.3 0.7 - - - +
121B ILE 3.4 7.6 - - - +
122B TYR* 3.9 35.2 - - + -
153B ASP* 5.2 2.5 - - - +
155B LEU* 4.5 9.2 - - + -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PRO* 3.7 31.9 - - + -
26B VAL* 3.8 20.6 - - + -
33B VAL* 4.0 33.0 - - + -
34B LEU 4.2 1.6 - - - -
35B GLY* 3.7 13.9 - - - -
48B ALA* 3.9 24.7 - - + -
49B ILE* 1.3 80.7 - - - +
51B LEU* 1.3 66.6 + - - +
53B ILE* 3.8 19.1 - - + -
80B ALA* 3.7 6.1 - - + -
119B LEU 4.4 0.2 - - - +
120B ASN* 3.3 5.9 - - - -
121B ILE* 2.9 43.1 + - + +
123B THR* 4.3 3.1 - - + -
127B LEU* 4.6 0.4 - - + -
208B PHE* 3.8 24.7 - + - -
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Residues in contact with LEU 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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36B LYS* 4.7 15.9 - - - +
49B ILE* 4.0 20.2 - - + -
50B PHE* 1.3 83.0 - - - +
52B GLY* 1.3 65.3 + - - +
53B ILE 3.6 0.9 - - - -
80B ALA* 3.0 29.1 + - - +
81B THR* 3.6 14.8 + - - +
82B SER 3.7 22.6 - - - +
83B TYR* 3.5 54.3 - - + +
120B ASN* 3.5 19.7 - - + +
122B TYR* 4.1 4.7 - - - +
1282B SIA 3.9 2.1 + - - -
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Residues in contact with GLY 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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51B LEU* 1.3 73.9 - - - +
53B ILE* 1.3 61.1 + - - +
54B PRO* 3.4 5.7 - - - +
78B LYS* 5.0 1.6 - - - +
80B ALA* 4.9 2.4 - - - +
84B PRO* 3.7 13.0 - - - +
118B TYR* 3.3 22.7 - - - -
119B LEU 3.8 0.6 + - - -
120B ASN* 3.0 13.3 + - - -
1282B SIA 3.5 32.8 + - - -
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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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28B THR* 5.9 0.2 - - + -
33B VAL* 3.8 26.5 - - + -
50B PHE* 3.8 24.5 - - + -
51B LEU 4.9 0.7 - - - +
52B GLY* 1.3 75.8 - - - +
54B PRO* 1.3 77.2 - - + +
55B PHE 3.6 0.3 + - - -
74B TRP* 4.9 5.8 - - + -
78B LYS* 5.5 0.4 - - - -
80B ALA* 3.8 19.5 - - + -
118B TYR* 3.4 1.4 - - - -
119B LEU* 3.1 37.9 + - + +
121B ILE* 4.2 8.7 - - + -
200B TRP* 3.7 26.5 - - + +
208B PHE* 3.9 22.9 - - + -
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Residues in contact with PRO 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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30B HIS* 5.1 0.3 - - - -
52B GLY 3.4 9.2 - - - +
53B ILE* 1.3 95.1 - - + +
55B PHE* 1.3 60.8 + - - +
56B ALA 4.2 12.8 - - - +
58B PRO* 6.5 0.2 - - + -
71B ALA* 4.2 11.9 - - + +
74B TRP* 3.7 26.0 - - + -
78B LYS* 4.0 24.9 - - + +
117B LEU 3.9 3.1 - - - +
118B TYR* 3.8 23.3 - - + -
200B TRP* 3.8 8.0 + - - -
1282B SIA 5.6 0.2 - - - +
183C GLU* 4.7 5.4 - - - +
184C HIS* 6.1 3.8 - - + +
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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