Contacts of the strand formed by residues 59 - 66 (chain A) in PDB entry 4X4R
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 GLU 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A SER* 4.6 1.9 + - - -
48A TYR* 3.7 14.5 - - - +
53A TRP* 5.2 1.7 - - - +
57A SER 3.4 7.1 + - - +
58A LEU* 1.3 77.8 - - - +
60A ILE* 1.3 68.6 + - - +
61A ASP* 3.0 22.9 + - - +
101A HIS* 4.1 10.7 - - - -
108A GLU* 3.4 24.9 - - + +
110A ASP* 3.8 24.0 - - - +
501A APC 3.6 7.9 + - - +
502A MG 3.1 28.9 - - - -
37B C 4.9 4.6 + - - +
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Residues in contact with ILE 60 (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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24A GLY* 3.9 21.5 - - - +
27A ALA* 4.1 1.6 - - + -
28A GLU* 4.1 14.6 - - - +
31A LEU* 3.9 11.4 - - + -
44A PHE* 3.6 33.2 - - + -
48A TYR* 4.1 26.2 - - + -
58A LEU* 4.8 4.9 - - + -
59A GLU* 1.3 76.7 - - - +
61A ASP* 1.3 65.6 + - - +
62A VAL* 4.2 1.1 - - + -
107A VAL* 3.6 26.7 - - + -
108A GLU 2.7 15.1 + - - +
109A VAL* 3.2 9.4 - - + +
110A ASP 2.9 26.0 + - - +
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Residues in contact with ASP 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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44A PHE* 3.8 4.7 - - - -
45A VAL* 3.4 45.8 + - + +
46A GLY* 4.1 6.8 - - - -
47A SER 4.6 0.2 + - - -
48A TYR* 5.1 0.4 + - - +
59A GLU* 3.0 20.1 + - - +
60A ILE* 1.3 78.3 - - - +
62A VAL* 1.3 65.8 + - - +
63A PHE* 4.2 2.2 - - + -
110A ASP* 3.6 6.7 - - - +
501A APC 2.9 16.0 + - - -
502A MG 2.7 26.2 - - - -
37B C 2.8 29.4 - - - +
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Residues in contact with VAL 62 (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 34.1 - - + -
35A LEU* 3.7 25.4 - - + -
42A TYR* 4.3 6.1 - - + -
43A VAL 3.8 5.8 - - - +
44A PHE* 4.0 13.7 - - + -
60A ILE* 4.2 1.8 - - + -
61A ASP* 1.3 79.4 - - - +
63A PHE* 1.3 67.7 + - - +
64A LEU* 3.9 16.1 + - + -
109A VAL* 4.4 5.6 - - + -
110A ASP 2.8 12.5 + - - +
111A VAL* 3.4 11.6 - - + +
112A VAL 2.9 25.6 + - - -
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Residues in contact with PHE 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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42A TYR* 3.1 6.8 - - - +
43A VAL* 2.9 52.8 + - + +
45A VAL* 3.5 24.7 - - + -
61A ASP* 4.2 1.3 - - + -
62A VAL* 1.3 78.8 - - - +
64A LEU* 1.3 59.0 - - - +
65A LEU* 4.0 0.6 + - + -
112A VAL* 3.3 33.0 - - + -
114A CYS* 3.4 26.2 - - + -
127A VAL* 3.3 33.7 - - + -
130A THR* 3.5 11.2 - - + -
131A PRO* 3.9 9.0 - - + -
37B C 3.3 32.3 - - - -
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Residues in contact with LEU 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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35A LEU* 4.1 19.5 - - + -
40A VAL* 4.5 8.1 - - + -
41A GLU 3.7 4.0 - - - +
42A TYR* 3.8 21.8 - - + -
62A VAL* 4.2 6.7 - - + -
63A PHE* 1.3 74.0 - - - +
65A LEU* 1.3 61.5 + - - +
66A PHE* 3.6 23.3 - - + -
79A GLY* 4.2 9.4 - - - +
82A ILE* 3.4 37.9 - - + -
111A VAL* 3.7 22.2 - - + -
112A VAL 2.9 13.9 + - - +
113A PRO* 4.6 0.4 - - + -
114A CYS* 3.0 29.7 + - - +
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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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41A GLU* 2.9 48.5 + - + +
42A TYR* 3.7 23.3 - - - +
43A VAL* 3.8 14.8 - - + +
63A PHE 4.1 1.1 - - - +
64A LEU* 1.3 72.7 - - - +
66A PHE* 1.3 64.6 + - - +
67A PRO* 4.7 0.3 - - - +
114A CYS* 3.6 19.1 - - - -
115A TYR 4.6 0.9 - - - +
116A LYS* 3.8 40.9 - - + +
117A LEU 5.4 0.2 - - - +
131A PRO* 4.5 17.7 - - + -
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Residues in contact with PHE 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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40A VAL* 5.4 6.3 - - + -
64A LEU* 3.6 39.5 - - + -
65A LEU* 1.3 77.5 - - - +
67A PRO* 1.3 74.5 - - + +
70A PHE* 3.8 24.0 - + + -
75A LEU* 3.7 30.3 - - + -
78A ARG* 3.9 43.3 - - + -
79A GLY* 4.1 20.2 - - - -
82A ILE* 4.4 5.4 - - + -
113A PRO* 4.2 4.5 - - + -
114A CYS 3.0 6.9 + - - -
115A TYR* 3.5 2.6 - - - -
116A LYS* 2.8 26.7 + - - +
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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