Contacts of the helix formed by residues 77 - 84 (chain A) in PDB entry 4TLG
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 PRO 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A TRP* 4.4 1.6 - - + -
75A GLN 4.6 0.2 - - - +
76A PRO* 1.3 91.0 - - + +
78A GLU* 1.3 66.9 + - - +
79A VAL* 4.4 14.6 - - + +
80A ILE* 3.0 17.2 + - + +
81A GLN 3.0 18.4 + - - -
114A SER 5.5 1.3 - - - +
115A ALA* 4.5 7.2 - - + -
119A ASP* 3.3 35.0 - - + +
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Residues in contact with GLU 78 (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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76A PRO 3.6 1.4 + - - -
77A PRO* 1.3 71.3 - - - +
79A VAL* 1.3 62.7 + - - +
81A GLN* 3.2 12.4 + - + +
82A LEU* 2.9 42.2 + - + +
268A TYR* 2.8 32.1 + - + +
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Residues in contact with VAL 79 (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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77A PRO* 4.4 5.6 - - + +
78A GLU* 1.3 78.2 - - - +
80A ILE* 1.3 63.5 + - + +
82A LEU* 4.9 0.2 - - - -
83A TYR* 2.9 37.2 + - + +
111A LEU* 3.7 11.6 - - + +
114A SER* 3.7 30.5 - - - +
115A ALA* 3.9 15.7 - - + -
264A VAL* 3.6 31.4 - - + -
268A TYR* 3.7 30.5 - - + -
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Residues in contact with ILE 80 (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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76A PRO* 3.7 18.8 - - + -
77A PRO* 3.0 14.8 + - + +
79A VAL* 1.3 77.4 - - + +
81A GLN* 1.3 66.4 + - - +
84A ASP* 3.0 52.4 + - + +
111A LEU* 4.4 8.1 - - + -
115A ALA* 3.9 24.2 - - + -
119A ASP* 3.5 41.7 - - + +
120A MET* 3.9 10.8 - - + +
123A LYS* 3.9 18.1 - - + -
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Residues in contact with GLN 81 (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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75A GLN* 3.9 29.8 + - - +
76A PRO* 2.8 43.4 + - + +
77A PRO 3.0 9.3 + - - +
78A GLU* 3.6 11.5 - - + +
80A ILE* 1.3 76.9 - - - +
82A LEU* 1.3 66.3 + - + +
84A ASP 5.0 0.7 - - - +
259A ASN* 3.6 11.6 + - - -
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Residues in contact with LEU 82 (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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78A GLU* 2.9 36.0 + - + +
81A GLN* 1.3 83.8 - - + +
83A TYR* 1.3 81.6 + - + +
259A ASN* 2.9 18.7 + - - +
261A GLY 4.7 2.1 - - - +
268A TYR* 3.5 25.6 - - + +
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Residues in contact with TYR 83 (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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79A VAL* 2.9 28.4 + - + +
82A LEU* 1.3 98.5 - - + +
84A ASP* 1.3 62.6 + - - +
85A SER 3.3 1.2 + - - -
106A LEU* 3.8 7.8 - - - +
107A ASP* 5.2 1.2 + - - +
111A LEU* 4.1 6.2 - - + +
259A ASN* 3.9 4.3 - - - -
261A GLY* 3.3 37.0 - - - -
262A GLY* 4.0 13.7 - - - +
263A GLU 3.8 14.1 - - - -
264A VAL* 3.9 19.7 - - + -
265A PRO* 3.3 31.5 - - + +
268A TYR* 3.8 19.0 + + - -
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Residues in contact with ASP 84 (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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79A VAL 4.0 0.8 + - - -
80A ILE* 3.0 40.6 + - + +
81A GLN 5.0 0.7 - - - +
83A TYR* 1.3 73.7 - - - +
85A SER* 1.3 67.9 + - - +
86A GLY 5.0 0.3 - - - +
106A LEU* 3.7 5.9 - - - +
111A LEU* 4.0 10.5 - - + +
120A MET* 4.0 13.0 - - - +
123A LYS* 2.9 32.7 + - - +
124A ARG* 2.9 41.4 + - - -
259A ASN* 3.6 11.4 + - - +
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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