Contacts of the helix formed by residues 80 - 96 (chain T) in PDB entry 5L4K
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 80 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79T GLY* 1.3 96.4 - - - +
81T ALA* 1.3 58.9 + - - +
82T ALA* 3.2 13.5 - - + +
83T THR* 3.0 28.6 + - + +
84T SER* 2.9 13.9 + - - -
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Residues in contact with ALA 81 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80T PRO* 1.3 71.8 - - - +
82T ALA* 1.3 57.0 + - - +
83T THR 3.5 0.2 - - - -
84T SER* 3.8 10.0 - - - -
85T GLY* 2.9 20.9 + - - -
136T LEU* 4.3 24.9 - - + -
140T GLN* 4.4 15.6 + - - +
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Residues in contact with ALA 82 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80T PRO* 3.2 7.9 - - + +
81T ALA* 1.3 77.0 - - - +
83T THR* 1.3 61.5 + - + +
85T GLY* 3.6 4.0 + - - +
86T ALA* 2.9 22.5 + - - +
89T GLN* 5.6 1.0 + - - -
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Residues in contact with THR 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79T GLY* 3.4 15.5 - - - -
80T PRO* 3.0 32.5 + - + -
82T ALA* 1.3 75.4 - - + +
84T SER* 1.3 63.5 + - - +
86T ALA* 3.0 12.0 + - + +
87T VAL* 2.9 30.6 + - - +
126T LEU* 5.0 3.8 - - - +
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Residues in contact with SER 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79T GLY 3.8 2.9 + - - -
80T PRO 2.9 17.2 + - - -
81T ALA* 3.8 11.1 - - - -
83T THR* 1.3 78.6 + - - +
85T GLY* 1.3 61.7 + - - -
87T VAL* 2.9 14.7 + - - +
88T LEU* 3.0 18.3 + - - +
126T LEU* 3.2 39.8 + - - +
128T PHE* 4.2 18.8 - - - -
140T GLN* 4.4 2.5 - - - -
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Residues in contact with GLY 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81T ALA 2.9 20.4 + - - -
82T ALA* 3.6 4.7 - - - -
83T THR 3.3 0.4 - - - -
84T SER* 1.3 74.2 - - - +
86T ALA* 1.3 55.7 + - - +
88T LEU* 3.0 36.7 + - - +
89T GLN* 3.0 28.4 + - - +
140T GLN* 5.4 0.9 - - - -
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Residues in contact with ALA 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82T ALA 2.9 17.2 + - - +
83T THR* 3.0 17.7 + - + +
85T GLY* 1.3 75.0 - - - +
87T VAL* 1.3 58.7 + - - +
89T GLN* 4.3 12.5 - - - +
90T ALA* 3.7 17.0 + - - +
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Residues in contact with VAL 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83T THR 2.9 14.6 + - - +
84T SER 2.9 7.8 + - - +
86T ALA* 1.3 79.5 - - + +
88T LEU* 1.3 64.7 + - + +
89T GLN 3.3 0.2 - - - -
90T ALA* 3.1 7.8 + - + +
91T ALA* 2.9 20.4 + - + +
119T LEU* 3.6 25.9 - - + +
122T VAL* 4.0 22.4 - - + -
123T LEU* 4.9 12.6 - - + -
126T LEU* 4.0 21.8 - - + -
147T ILE* 6.1 0.4 - - + -
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Residues in contact with LEU 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84T SER 3.0 14.4 + - - +
85T GLY* 3.0 17.7 + - - +
87T VAL* 1.3 75.9 - - - +
89T GLN* 1.3 59.5 + - + +
91T ALA* 2.9 22.2 + - - +
92T THR* 2.9 15.2 + - - -
95T TYR* 4.8 2.3 + - - -
123T LEU* 4.2 22.7 - - + -
128T PHE* 4.8 5.4 - - + -
140T GLN* 3.5 29.8 - - - +
143T LEU* 3.6 49.4 - - + +
147T ILE* 4.8 4.2 - - + +
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Residues in contact with GLN 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82T ALA 5.6 0.6 + - - -
85T GLY* 3.0 22.4 + - - +
86T ALA* 4.7 8.2 - - - +
88T LEU* 1.3 76.7 - - + +
90T ALA* 1.3 55.8 + - - +
91T ALA 3.1 0.2 - - - -
92T THR* 2.9 27.7 + - - +
93T GLY* 3.0 11.8 + - - -
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Residues in contact with ALA 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86T ALA 3.7 15.1 + - - +
87T VAL* 3.1 16.4 + - + +
89T GLN* 1.3 76.1 - - - +
91T ALA* 1.3 55.7 + - - +
93T GLY* 4.1 4.3 + - - +
94T MET* 3.4 27.7 - - + +
119T LEU* 3.5 16.1 - - + +
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Residues in contact with ALA 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87T VAL* 2.9 8.6 + - + +
88T LEU 2.9 11.2 + - - +
90T ALA* 1.3 76.5 - - - +
92T THR* 1.3 58.0 + - - +
93T GLY 3.3 1.1 - - - -
94T MET* 3.2 2.6 + - - +
95T TYR* 2.9 38.7 + - + +
116T LEU* 4.2 12.2 - - + +
119T LEU* 4.0 12.8 - - + -
147T ILE* 3.6 35.4 - - + -
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Residues in contact with THR 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88T LEU 2.9 11.4 + - - -
89T GLN* 2.9 17.0 + - - +
91T ALA* 1.3 75.0 - - - +
93T GLY* 1.3 59.8 + - - +
94T MET 3.1 1.8 - - - -
95T TYR* 3.4 28.9 + - + +
96T GLU* 3.3 29.6 + - + +
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Residues in contact with GLY 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89T GLN 3.0 12.7 + - - -
90T ALA* 4.1 3.7 - - - -
91T ALA 3.3 0.6 - - - -
92T THR* 1.3 76.3 - - - +
94T MET* 1.3 65.1 + - - +
96T GLU* 4.7 1.1 - - - -
97T GLN* 3.2 31.8 + - - +
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Residues in contact with MET 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90T ALA* 3.4 20.9 - - + +
91T ALA 3.2 2.6 + - - +
92T THR 3.1 0.4 - - - -
93T GLY* 1.3 88.5 - - - +
95T TYR* 1.3 59.9 + - - +
96T GLU 3.5 1.6 - - - -
97T GLN* 3.9 17.0 - - - +
98T LEU* 3.3 18.5 + - - +
112T CYS* 3.5 27.0 - - + +
115T GLU* 5.1 17.0 - - + -
116T LEU* 3.9 23.5 - - + +
118T ARG* 5.7 5.2 - - - +
119T LEU* 4.2 10.8 - - + -
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Residues in contact with TYR 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88T LEU 4.8 1.6 + - - -
91T ALA* 2.9 30.9 + - + -
92T THR* 3.4 29.8 + - + -
94T MET* 1.3 75.4 - - - +
96T GLU* 1.3 61.9 + - + +
97T GLN 3.6 0.2 - - - -
98T LEU* 4.0 8.3 - - - -
99T LYS* 2.9 30.3 - - + +
116T LEU* 3.9 15.3 - - + -
143T LEU* 5.1 6.0 + - - +
146T ASP* 4.5 20.0 + - + -
147T ILE* 3.8 34.8 - - + -
150T ILE* 4.2 29.8 - - + +
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Residues in contact with GLU 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92T THR* 3.3 24.5 + - + +
93T GLY* 5.5 0.4 - - - -
95T TYR* 1.3 78.6 - - + +
97T GLN* 1.3 58.8 + - + +
98T LEU 3.3 1.3 - - - -
99T LYS* 3.4 32.6 + - + +
100T GLY* 3.0 21.3 + - - -
103T ASN* 5.8 0.3 + - - -
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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