Contacts of the helix formed by residues 82 - 94 (chain F) in PDB entry 2CSL
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 ASP 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45F ILE* 3.1 40.0 - - + +
77F LEU* 4.5 4.3 - - + -
78F ALA* 5.8 0.5 - - - +
79F ASP* 2.7 30.0 + - - +
81F GLU* 1.3 79.8 - - - +
83F PHE* 1.3 64.2 + - - +
84F PRO* 3.4 2.7 - - - -
85F GLY 3.4 2.8 + - - +
86F PHE* 3.0 22.3 + - - +
114F ARG* 3.1 39.3 + - - +
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Residues in contact with PHE 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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110E PRO* 6.4 0.4 - - + -
77F LEU* 3.9 11.6 - - + +
80F MSE 3.0 45.6 + - + +
82F ASP* 1.3 76.9 - - - +
84F PRO* 1.3 63.7 - - + +
86F PHE* 3.0 16.5 + + - +
87F ASN* 2.6 71.0 + - + +
101F ARG* 3.8 13.0 - - - -
103F THR* 4.0 26.0 - - + -
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Residues in contact with PRO 84 (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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46F ARG* 4.6 5.6 - - - +
80F MSE 4.3 0.7 - - - +
81F GLU* 3.4 17.9 - - - +
82F ASP 3.5 1.1 - - - -
83F PHE* 1.3 100.4 - - + +
85F GLY* 1.3 63.7 + - - +
87F ASN* 3.3 2.9 + - + +
88F GLU* 2.9 26.1 + - - +
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Residues in contact with GLY 85 (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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45F ILE* 3.7 19.4 - - - +
46F ARG* 3.6 33.6 - - - +
82F ASP 3.4 3.6 + - - -
83F PHE 3.4 0.2 - - - -
84F PRO* 1.3 78.5 - - - +
86F PHE* 1.3 63.9 + - - +
88F GLU* 3.4 2.8 + - - +
89F VAL* 3.3 26.9 + - - +
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Residues in contact with PHE 86 (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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45F ILE* 4.2 3.4 - - + +
49F THR* 3.5 37.7 - - + +
53F MSE 4.2 3.1 - - + -
75F CYS* 3.7 34.8 - - + -
77F LEU* 3.9 16.6 - - + -
82F ASP 3.0 14.8 + - - +
83F PHE* 3.3 30.1 - + - +
85F GLY* 1.3 78.6 - - - +
87F ASN* 1.3 60.6 + - - +
89F VAL* 3.3 0.9 + - - -
90F TYR* 2.9 54.5 + + - +
101F ARG* 4.4 9.0 - - - -
103F THR* 4.6 2.0 - - + -
115F VAL* 3.6 27.4 - - + -
117F VAL* 3.9 8.3 - - + -
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Residues in contact with ASN 87 (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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13E ILE 5.4 1.8 + - - -
14E GLY* 5.0 3.6 - - - -
15E PRO* 3.5 19.6 - - - +
83F PHE* 2.6 47.3 + - + +
84F PRO* 3.8 4.3 - - + +
86F PHE* 1.3 75.7 - - - +
88F GLU* 1.3 63.4 + - - +
90F TYR* 3.5 4.2 - - - +
91F ALA* 2.9 26.0 + - - +
101F ARG* 2.8 36.5 + - - +
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Residues in contact with GLU 88 (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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46F ARG* 3.3 37.8 + - - -
84F PRO 2.9 17.8 + - - +
85F GLY 3.7 4.0 - - - +
86F PHE 3.2 0.2 - - - -
87F ASN* 1.3 79.1 - - - +
89F VAL* 1.3 64.0 + - - +
91F ALA* 3.4 15.2 - - - +
92F ARG* 3.7 28.2 + - - +
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Residues in contact with VAL 89 (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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46F ARG* 3.5 38.1 - - + +
49F THR* 3.8 15.0 - - + -
50F GLU* 3.8 24.5 - - - +
53F MSE 4.1 1.1 - - + -
85F GLY 3.3 13.4 + - - +
86F PHE 3.9 0.9 - - - +
88F GLU* 1.3 73.0 - - + +
90F TYR* 1.3 67.5 + - - +
92F ARG* 2.9 44.4 + - - +
93F TYR* 3.3 24.0 - - + -
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Residues in contact with TYR 90 (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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15E PRO* 3.6 30.1 - - + -
49F THR* 4.4 0.6 - - - +
53F MSE 3.7 24.2 - - + -
73F THR* 2.7 33.5 + - + +
75F CYS* 4.1 17.0 - - - -
86F PHE* 2.9 37.7 + + + +
87F ASN* 3.5 8.1 - - - +
89F VAL* 1.3 75.6 - - - +
91F ALA* 1.3 61.7 + - - +
92F ARG 3.1 1.0 + - - -
93F TYR* 3.2 11.8 + - - +
94F PHE* 3.4 40.6 + + - -
99F PRO* 4.3 8.0 + - - +
101F ARG* 3.1 34.2 - - - +
117F VAL* 5.0 1.3 - - + -
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Residues in contact with ALA 91 (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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15E PRO* 3.4 28.3 - - + -
87F ASN 2.9 17.7 + - - +
88F GLU* 3.4 10.1 - - - +
89F VAL 3.1 0.2 - - - -
90F TYR* 1.3 76.4 - - - +
92F ARG* 1.3 62.0 + - - +
94F PHE 3.5 15.8 - - - +
98F TYR* 4.8 5.5 + - - +
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Residues in contact with ARG 92 (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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46F ARG* 4.5 8.1 + - - +
50F GLU* 3.4 24.0 + - - +
88F GLU* 3.7 30.5 + - - +
89F VAL* 2.9 45.0 + - - +
91F ALA* 1.3 79.6 - - - +
93F TYR* 1.3 75.1 + - + +
94F PHE 3.6 2.4 + - - +
95F THR* 5.6 0.5 + - - -
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Residues in contact with TYR 93 (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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50F GLU* 3.7 23.0 + - - +
53F MSE 3.5 46.0 - - + -
54F GLU* 3.0 31.8 + - - -
57F LYS* 5.4 4.5 - - + -
67F LEU* 3.7 49.5 - - + +
89F VAL* 3.3 29.2 - - + -
90F TYR 3.2 5.3 + - - +
92F ARG* 1.3 91.2 + - + +
94F PHE* 1.3 61.0 + - + +
95F THR* 4.1 1.3 + - - -
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Residues in contact with PHE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E PRO* 5.0 0.4 - - + -
53F MSE 3.9 14.4 - - + -
56F LEU* 4.5 11.0 - - + -
67F LEU* 3.7 35.7 - - + -
70F VAL* 3.7 27.6 - - + -
73F THR* 4.1 14.4 - - + -
90F TYR* 3.4 57.4 + + + +
91F ALA 3.5 10.2 + - - +
92F ARG 3.5 2.1 - - - +
93F TYR* 1.3 80.9 - - + +
95F THR* 1.3 64.7 + - - +
96F PRO* 4.6 0.3 - - - +
98F TYR* 3.2 23.7 + - + -
99F PRO* 3.5 29.2 - - + -
119F CYS* 5.8 0.7 - - + -
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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