Contacts of the strand formed by residues 63 - 70 (chain A) in PDB entry 5Y1Z
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 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR* 2.9 19.9 + - - -
34A TYR* 3.6 36.9 - - + -
62A LYS* 1.3 72.8 + - - +
64A MET* 1.3 62.7 + - - +
65A TYR* 3.8 20.0 - - + +
84A ASN* 5.0 0.9 - - - +
85A TRP 3.3 10.3 - - - +
86A VAL* 4.2 15.9 - - + -
90A VAL* 3.8 28.9 - - + +
94A ARG* 4.5 6.3 - - + +
95A LYS* 5.1 0.4 - - - -
98A CYS* 3.9 24.2 - - + -
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Residues in contact with MET 64 (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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31A LEU* 3.4 26.5 - - + -
32A TYR 3.2 10.8 - - - +
33A THR* 3.5 19.1 - - - +
44A ALA* 5.4 1.8 - - - -
57A HIS 3.5 1.3 - - - +
58A PHE* 3.2 44.6 - - + -
59A GLU* 3.7 33.2 - - - +
62A LYS* 3.8 11.2 + - + -
63A VAL* 1.3 80.0 - - - +
65A TYR* 1.3 70.7 + - - +
83A ILE 3.5 0.2 - - - +
85A TRP* 2.9 45.0 + - + +
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Residues in contact with TYR 65 (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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31A LEU* 3.6 4.3 - - - -
32A TYR* 2.8 51.5 + - + +
33A THR* 5.3 0.2 - - - -
34A TYR* 2.6 43.3 + + - -
41A LEU* 4.0 19.3 - - + -
63A VAL* 3.8 14.4 - - + +
64A MET* 1.3 79.1 - - - +
66A GLY* 1.3 60.2 + - - +
82A LEU* 4.1 18.8 - - + -
83A ILE 3.3 6.7 - - - -
84A ASN* 3.4 26.0 + - + -
98A CYS* 3.5 17.3 + - - +
101A HIS* 3.9 2.8 - - + +
102A VAL* 4.0 14.9 - - + +
105A VAL* 4.0 32.5 - - + -
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Residues in contact with GLY 66 (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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30A ALA 3.6 6.7 - - - -
31A LEU* 4.1 10.9 - - - +
54A LEU* 4.3 14.4 - - - -
58A PHE* 4.6 1.9 - - - -
64A MET 4.2 0.4 - - - -
65A TYR* 1.3 71.6 - - - +
67A PHE* 1.3 59.7 + - - -
68A CYS 3.8 1.0 + - - -
81A VAL 3.2 2.1 - - - +
82A LEU* 3.1 8.9 - - - +
83A ILE* 2.8 47.5 + - - +
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Residues in contact with PHE 67 (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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17A TYR* 3.4 37.9 - + - -
20A VAL* 3.5 31.0 - - + +
21A ILE* 3.7 9.2 - - + -
28A ASP 4.1 0.2 - - - +
29A TRP* 3.3 2.4 - - - -
30A ALA* 2.8 40.0 + - + +
32A TYR* 4.4 17.0 - - + -
65A TYR 4.0 0.8 + - - -
66A GLY* 1.3 71.0 - - - -
68A CYS* 1.3 58.5 + - - +
80A TYR* 3.5 30.7 - + + -
81A VAL 3.5 7.6 - - - -
82A LEU* 4.5 8.7 - - + -
109A PHE* 3.8 29.2 - + + -
110A GLN 4.6 1.8 - - - -
112A VAL* 3.9 18.4 - - + -
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Residues in contact with CYS 68 (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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20A VAL* 4.6 0.4 - - - -
28A ASP 3.3 11.7 - - - -
29A TRP* 4.0 8.3 - - + -
50A GLY* 3.9 8.7 - - - -
51A LEU* 3.7 50.0 - - + -
54A LEU* 4.1 7.9 - - + -
66A GLY 3.8 0.4 + - - +
67A PHE* 1.3 75.3 - - - +
69A SER* 1.3 73.3 + - - +
70A VAL* 3.9 3.8 + - - -
80A TYR* 3.6 5.9 - - - -
81A VAL* 3.0 40.2 + - + +
83A ILE* 5.4 0.4 - - + -
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Residues in contact with SER 69 (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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20A VAL* 3.7 20.8 + - - +
28A ASP* 2.8 30.0 + - - +
50A GLY* 5.2 0.5 - - - -
68A CYS* 1.3 81.0 - - - +
70A VAL* 1.3 65.3 + - - +
71A LYS* 4.4 0.3 + - - +
78A PRO* 3.5 21.8 - - - +
79A LYS 3.7 5.4 - - - -
80A TYR* 3.4 22.4 + - - -
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Residues in contact with VAL 70 (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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51A LEU* 4.3 20.4 - - + +
68A CYS* 4.2 14.6 - - - +
69A SER* 1.3 79.8 + - - +
71A LYS* 1.3 71.1 + - - +
77A LEU 4.8 0.2 - - - +
78A PRO* 3.4 3.9 - - - +
79A LYS* 2.9 39.4 + - + +
81A VAL* 4.3 15.7 - - + -
129A ILE* 5.3 1.6 - - + -
130A GLY* 5.7 5.4 - - - -
133A LEU* 4.5 20.0 - - + -
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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