Contacts of the strand formed by residues 60 - 69 (chain A) in PDB entry 2P6Y
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 PHE 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A CYS* 3.2 6.8 - - - +
40A LEU* 2.8 43.8 + - + +
43A LEU* 3.7 36.6 - - + -
54A LEU* 6.4 0.2 - - + -
56A VAL* 3.7 38.8 - - + -
58A ALA* 3.1 33.7 - - + -
59A PRO* 1.3 76.8 - - - +
61A GLU* 1.3 63.3 + - - +
80A VAL* 3.7 31.0 - - + -
81A ALA 3.2 14.6 - - - +
82A ASP* 3.8 21.5 - - + -
88A TRP* 4.5 10.5 - + - -
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Residues in contact with GLU 61 (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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38A GLY 3.7 5.3 - - - +
39A CYS* 3.4 22.9 - - - +
60A PHE* 1.3 72.3 - - - +
62A ILE* 1.3 62.7 + - - +
63A LEU* 3.4 14.9 + - + +
80A VAL* 3.1 7.3 - - - -
81A ALA* 2.9 40.6 + - + +
82A ASP 5.8 1.8 - - - +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.3 14.8 - - + -
36A CYS* 3.2 37.3 - - + +
37A VAL* 4.3 6.9 - - - +
38A GLY* 2.8 39.6 + - - +
39A CYS* 4.0 2.9 - - - +
40A LEU* 3.9 40.6 - - + -
61A GLU* 1.3 72.0 - - - +
63A LEU* 1.3 63.4 + - - +
64A SER 4.2 15.7 - - - +
65A LEU* 4.8 1.8 - - + -
78A ILE* 4.1 17.0 - - + -
79A ALA 4.0 2.7 - - - -
80A VAL* 4.2 2.2 - - + -
98A ILE* 4.7 5.8 - - + -
102A ALA* 4.8 1.3 - - + -
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Residues in contact with LEU 63 (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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36A CYS 5.7 1.7 - - - -
37A VAL* 6.0 2.8 - - - +
61A GLU* 3.9 18.8 - - + +
62A ILE* 1.3 79.9 - - - +
64A SER* 1.3 64.7 + - - +
79A ALA* 2.9 17.8 + - + +
81A ALA* 3.9 17.7 - - + +
87A VAL* 3.5 39.7 - - + -
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Residues in contact with SER 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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36A CYS 5.9 2.5 - - - +
62A ILE* 3.7 4.4 - - - -
63A LEU* 1.3 82.9 - - - +
65A LEU* 1.3 62.5 + - - +
66A SER* 4.3 5.1 + - - -
77A HIS 4.7 0.2 - - - -
78A ILE* 3.5 8.1 - - - +
79A ALA* 3.0 44.3 + - - +
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Residues in contact with LEU 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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15A LEU* 4.3 7.2 - - + -
19A ILE* 3.7 29.8 - - + -
33A ILE* 3.3 36.2 - - + +
34A ALA 5.6 0.2 - - - -
35A SER* 5.4 1.4 + - - -
36A CYS* 3.9 39.1 - - + +
62A ILE* 4.8 1.3 - - + -
64A SER* 1.3 76.9 - - - +
66A SER* 1.3 61.3 + - - +
76A LEU* 4.2 16.8 - - + -
77A HIS 3.5 17.3 - - - +
78A ILE* 3.8 24.2 - - + -
92A LEU* 4.4 7.9 - - + -
104A LEU* 4.6 0.4 - - + -
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Residues in contact with SER 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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33A ILE* 4.1 4.9 - - - -
64A SER* 4.3 5.0 + - - -
65A LEU* 1.3 76.6 + - - +
67A GLY* 1.3 59.3 + - - +
75A HIS 3.9 0.3 - - - +
76A LEU* 3.3 4.3 - - - +
77A HIS* 2.9 40.4 + - - +
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Residues in contact with GLY 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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32A SER* 3.3 29.9 - - - -
33A ILE* 3.7 8.9 - - - +
66A SER* 1.3 77.9 - - - +
68A THR* 1.3 63.9 + - - -
69A LEU* 3.8 2.9 - - - -
75A HIS 3.1 11.2 - - - -
76A LEU* 3.7 14.6 - - - -
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Residues in contact with THR 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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31A GLY 3.9 2.7 - - - -
67A GLY* 1.3 71.8 + - - -
69A LEU* 1.3 62.5 + - - +
70A THR* 4.4 7.1 - - + +
73A HIS 3.8 2.4 - - - +
74A CYS* 3.5 3.3 - - - -
75A HIS* 3.0 42.8 + - - +
114A PHE* 4.3 14.1 - - + -
116A ARG* 4.7 7.8 + - - +
127A LEU* 3.9 37.0 - - + +
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Residues in contact with LEU 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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19A ILE* 4.0 11.9 - - + -
23A VAL* 4.0 21.8 - - + -
28A ILE* 4.6 4.5 - - + -
30A ALA* 3.5 7.9 - - - -
31A GLY* 2.9 42.0 + - - +
32A SER* 3.8 18.8 - - - +
33A ILE* 4.2 10.1 - - + -
67A GLY 4.4 1.6 - - - -
68A THR* 1.3 78.8 - - - +
70A THR* 1.3 60.5 + - - +
73A HIS 4.2 1.1 - - - -
74A CYS* 3.6 25.1 - - + -
76A LEU* 4.3 7.4 - - + -
106A ILE* 3.5 39.7 - - + -
114A PHE* 3.6 5.7 - - - -
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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