Contacts of the strand formed by residues 76 - 83 (chain F) in PDB entry 3EBL
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 LEU 76 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69F ILE* 3.4 3.2 - - - -
70F ILE* 2.7 55.3 + - + +
71F ASP* 2.7 25.6 + - + +
74F VAL* 3.3 8.6 - - + -
75F GLY* 1.3 72.0 - - - +
77F GLU* 1.3 58.9 + - - +
152F VAL* 4.2 7.0 - - + -
153F ASN 3.4 31.0 - - - +
154F TYR* 4.2 0.7 - - - -
155F ARG* 5.8 2.2 - - + -
168F ASP* 3.4 57.2 - - + +
171F THR* 3.9 12.3 - - + -
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Residues in contact with GLU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ASP* 3.2 29.6 - - + +
68F HIS 3.4 16.1 + - - +
69F ILE* 4.1 21.5 - - + +
75F GLY 3.3 7.3 + - - +
76F LEU* 1.3 81.2 - - - +
78F VAL* 1.3 74.6 + - - +
153F ASN* 3.0 44.9 + - + +
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Residues in contact with VAL 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F PHE 3.7 0.2 - - - +
67F ASP* 3.3 6.0 - - - +
68F HIS* 2.8 40.5 + - + +
70F ILE* 3.8 38.1 - - + -
77F GLU* 1.3 81.2 - - - +
79F ARG* 1.3 59.8 - - - +
80F ILE* 3.7 29.6 - - + -
129F ALA* 5.3 0.9 - - - -
150F VAL* 3.8 24.0 - - + -
151F SER 3.1 11.7 - - - +
152F VAL* 4.2 14.8 - - + -
153F ASN* 5.3 0.4 - - - -
172F ALA* 4.9 0.7 - - + -
175F TRP* 4.6 1.1 - - + -
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Residues in contact with ARG 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F VAL 2.7 29.9 + - - -
54F PRO* 3.5 10.1 + - - +
55F ALA* 3.2 20.8 - - - +
65F SER* 4.0 16.2 - - - -
66F PHE 3.4 7.4 - - - +
67F ASP* 2.8 33.1 + - - +
78F VAL* 1.3 72.8 - - - +
80F ILE* 1.3 61.7 + - - +
81F TYR* 3.1 40.2 - - + +
129F ALA* 4.3 13.7 - - + +
130F SER* 3.5 26.5 - - - +
135F ASP* 3.0 19.3 + - - -
150F VAL* 3.5 0.9 - - - -
151F SER* 2.7 40.6 + - - +
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Residues in contact with ILE 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F SER* 3.1 5.5 - - - -
66F PHE* 2.8 53.8 + - + +
68F HIS* 4.1 17.3 - - + -
78F VAL* 3.7 21.8 - - + -
79F ARG* 1.3 71.3 - - - +
81F TYR* 1.3 64.8 + - - +
82F ARG* 5.3 3.8 - - + -
148F VAL* 3.8 24.2 - - + -
149F VAL 3.2 3.4 - - - +
150F VAL* 4.3 10.8 - - + -
175F TRP* 3.8 26.2 - - + -
182F MET* 4.5 8.5 - - + -
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Residues in contact with TYR 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F VAL* 4.2 2.0 - - + -
64F SER 3.3 8.1 - - - +
65F SER* 3.9 16.6 - - - -
79F ARG* 3.1 39.1 - - + -
80F ILE* 1.3 73.7 - - - +
82F ARG* 1.3 61.3 + - - +
129F ALA 3.5 9.2 + - - -
134F TYR 4.4 0.2 + - - -
135F ASP* 2.8 52.5 + - - -
138F CYS* 3.5 26.1 - - + +
139F ARG* 3.7 20.4 - - + -
142F VAL* 3.4 20.5 - - + +
148F VAL* 3.4 9.9 - - - +
149F VAL* 2.7 41.0 + - + +
151F SER* 3.9 7.6 - - - -
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Residues in contact with ARG 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F VAL* 4.2 1.1 - - - -
64F SER* 2.9 30.2 + - - -
66F PHE* 3.9 26.0 - - + -
80F ILE* 5.3 4.7 - - + -
81F TYR* 1.3 76.1 - - - +
83F ALA* 1.3 69.5 + - - +
84F ALA* 5.4 2.0 - - + -
142F VAL* 4.0 9.6 - - - +
147F GLY 4.3 3.4 - - - +
148F VAL* 4.4 17.9 - - + -
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Residues in contact with ALA 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F GLY 3.1 12.3 - - - +
63F VAL* 5.4 0.7 - - + -
82F ARG* 1.3 80.0 - - - +
84F ALA* 1.3 62.1 + - - +
142F VAL* 3.5 19.5 - - + +
146F LYS* 6.2 4.3 - - - -
147F GLY 4.5 2.0 + - - +
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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