Contacts of the strand formed by residues 71 - 77 (chain A) in PDB entry 5L5E
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 ILE 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.8 1.4 - - - -
67A LEU* 2.9 29.4 + - + -
68A THR* 3.0 29.2 + - + +
69A PRO 3.6 0.2 - - - -
70A ASP* 1.3 87.4 - - + +
72A GLY* 1.3 62.5 + - - +
105A PRO 3.5 24.0 - - - +
106A PRO 4.3 0.2 - - - -
107A THR* 3.9 28.9 - - + +
110A LEU* 3.7 28.9 - - + -
136A ILE* 3.6 24.0 - - + -
137A ALA 3.4 11.0 - - - +
138A GLY* 4.2 0.7 - - - -
139A HIS 4.7 2.0 - - - +
214A ILE* 4.5 0.2 - - - +
235A PHE* 4.2 5.4 - - - +
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Residues in contact with GLY 72 (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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45A ILE* 3.9 8.5 - - - -
65A SER 3.4 10.1 - - - -
67A LEU* 4.4 1.1 - - - -
71A ILE* 1.3 75.3 - - - +
73A ALA* 1.3 59.9 + - - +
136A ILE* 3.5 6.2 - - - +
137A ALA 2.8 32.8 + - - +
214A ILE* 3.8 6.0 - - - +
235A PHE* 3.6 19.5 - - - -
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Residues in contact with ALA 73 (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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45A ILE* 3.9 5.8 - - - +
64A VAL* 3.3 5.2 - - - +
65A SER 2.9 33.5 + - - +
67A LEU* 3.8 28.5 - - + -
72A GLY* 1.3 75.5 - - - +
74A VAL* 1.3 61.0 + - - +
82A TYR* 3.0 16.8 + - + +
86A VAL* 5.3 0.7 - - + -
134A LEU* 5.7 3.8 - - + -
135A LEU 3.4 9.0 - - - +
136A ILE* 4.0 9.6 - - + -
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Residues in contact with VAL 74 (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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34A SER* 4.1 14.1 - - - -
35A LEU 4.4 2.5 - - - +
45A ILE* 4.1 19.7 - - + -
46A ALA 4.3 2.9 - - - +
47A THR* 3.6 37.2 - - + -
63A LYS* 3.8 10.8 - - + +
64A VAL* 3.8 16.6 - - + -
73A ALA* 1.3 74.5 - - - +
75A TYR* 1.3 70.6 + - - +
82A TYR* 4.0 3.4 - - - -
134A LEU* 3.5 6.1 - - - +
135A LEU* 2.8 54.9 + - + +
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Residues in contact with TYR 75 (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 VAL 4.5 0.9 - - - +
34A SER* 3.0 21.2 + - - -
47A THR* 4.5 3.8 + - - -
61A LEU* 5.3 5.6 - - + +
63A LYS* 3.7 46.8 - - + +
74A VAL* 1.3 80.5 - - + +
76A SER* 1.3 80.5 + - - +
77A GLY 3.5 25.8 + - - -
79A GLY* 3.4 28.4 + - - -
82A TYR* 3.4 51.8 - + + -
132A VAL* 4.3 4.9 - - + -
133A SER 3.4 12.1 - - - +
134A LEU* 3.9 4.7 - - + -
164A ILE* 4.1 0.4 - - - -
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Residues in contact with SER 76 (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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28A VAL* 3.6 11.9 - - - +
32A VAL 2.6 27.6 + - - +
34A SER* 2.8 21.7 + - - -
63A LYS* 6.2 0.2 - - - +
75A TYR* 1.3 76.5 + - - +
77A GLY* 1.3 58.5 + - - +
132A VAL* 3.6 1.9 - - - -
133A SER 3.1 28.9 + - - -
164A ILE* 3.3 21.9 + - - -
165A GLY* 3.9 15.3 - - - -
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Residues in contact with GLY 77 (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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27A ALA 4.0 18.8 - - - -
28A VAL* 4.0 3.4 - - - -
31A GLY* 3.9 16.4 - - - -
32A VAL 4.8 0.9 + - - +
75A TYR* 3.5 10.2 + - - -
76A SER* 1.3 75.5 - - - +
78A MET* 1.3 64.1 + - - -
79A GLY 3.5 2.9 + - - -
131A GLY 3.6 8.3 - - - -
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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