Contacts of the helix formed by residues 91 - 103 (chain T) in PDB entry 6Y5D
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 THR 91 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45S GLY* 4.7 6.5 - - - -
47S GLY 5.7 0.2 - - - +
48S ALA* 3.6 9.2 - - - +
89T THR* 3.9 22.2 - - + +
90T ILE* 1.3 79.5 - - - +
92T SER* 1.3 64.2 + - - +
93T ARG* 3.0 18.0 + - - +
94T GLU* 2.6 35.1 + - - +
95T ILE* 3.3 15.4 + - - +
44V G 6.2 0.2 - - - +
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Residues in contact with SER 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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47S GLY* 3.5 26.8 - - - -
48S ALA* 3.9 7.1 - - - +
51S TYR* 3.6 25.6 - - - -
91T THR* 1.3 75.5 + - - +
93T ARG* 1.3 60.8 + - - +
95T ILE* 3.6 2.1 - - - +
96T GLN* 2.9 28.7 + - - +
119T VAL* 3.9 16.2 - - - +
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Residues in contact with ARG 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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75R GLU* 2.8 35.8 + - - +
76R HIS* 3.0 36.8 + - + +
78R LYS* 3.5 30.1 - - - +
91T THR* 3.0 12.3 + - - +
92T SER* 1.3 80.0 + - - +
94T GLU* 1.3 64.7 + - - +
95T ILE 3.1 1.1 - - - -
96T GLN* 3.2 27.0 + - - +
97T THR* 2.9 30.5 + - - +
100T ARG* 5.3 2.4 - - - +
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Residues in contact with GLU 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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76R HIS* 3.8 25.6 + - + +
78T ALA* 3.9 33.4 - - + +
81T LEU* 3.2 15.4 - - + +
82T ALA* 4.1 10.6 - - + +
87T ARG* 4.0 20.3 + - - -
89T THR 4.0 10.1 - - - +
90T ILE* 4.1 4.9 - - + -
91T THR* 2.6 40.6 + - - +
93T ARG* 1.3 72.5 - - - +
95T ILE* 1.3 65.9 + - - +
98T ALA* 3.0 22.9 + - - +
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Residues in contact with ILE 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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35S LEU* 4.1 19.1 - - + -
48S ALA* 3.6 23.3 - - + +
51S TYR* 3.2 25.1 - - + -
52S MET* 3.8 26.7 - - + +
74T ILE* 3.9 11.7 - - + -
78T ALA* 3.9 11.4 - - + -
90T ILE* 3.8 18.2 - - + -
91T THR 3.3 13.2 + - - +
92T SER 3.6 7.2 - - - +
93T ARG 3.1 0.4 - - - -
94T GLU* 1.3 77.5 - - - +
96T GLN* 1.3 62.3 + - - +
98T ALA* 3.2 7.1 + - - +
99T VAL* 3.0 29.1 + - + +
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Residues in contact with GLN 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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51S TYR* 3.2 38.8 + - - +
92T SER* 2.9 19.4 + - - +
93T ARG* 3.3 29.8 + - - +
95T ILE* 1.3 76.9 - - - +
97T THR* 1.3 62.0 + - - +
99T VAL* 3.2 6.2 + - - +
100T ARG* 3.1 60.1 + - - +
112T VAL* 4.0 6.6 - - + +
116T THR* 4.4 8.3 + - - +
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Residues in contact with THR 97 (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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72R THR* 4.0 15.7 - - + +
76R HIS* 2.6 48.3 + - + +
81T LEU* 3.5 25.8 - - + -
93T ARG* 2.9 10.5 + - - +
96T GLN* 1.3 73.1 + - - +
98T ALA* 1.3 65.9 + - - +
100T ARG* 3.2 18.8 + - - +
101T LEU* 3.0 30.7 + - + +
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Residues in contact with ALA 98 (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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74T ILE* 3.5 24.5 - - + +
77T GLU* 3.3 32.1 - - + -
78T ALA 4.0 1.1 - - - +
81T LEU* 3.7 3.0 - - - +
94T GLU 3.0 18.6 + - - +
95T ILE 3.4 5.2 - - - +
97T THR* 1.3 75.9 - - - +
99T VAL* 1.3 57.9 + - - +
101T LEU* 3.2 3.9 + - - +
102T LEU* 2.8 37.0 + - - +
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Residues in contact with VAL 99 (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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51S TYR* 4.1 6.1 - - + -
55S VAL* 3.7 34.1 - - + -
74T ILE* 4.6 6.7 - - + -
95T ILE* 3.0 22.6 + - + +
96T GLN 3.3 8.1 - - - +
97T THR 3.1 0.4 - - - -
98T ALA* 1.3 77.2 - - - +
100T ARG* 1.3 58.3 + - - +
102T LEU* 4.8 1.3 - - - -
103T LEU* 2.9 44.2 + - + +
108T ALA* 3.5 24.2 - - - +
111T ALA* 3.6 18.4 - - + -
112T VAL* 3.8 7.4 - - + -
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Residues in contact with ARG 100 (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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68R ARG* 5.9 1.0 + - - -
69R ASP* 5.2 2.4 - - - +
72R THR* 4.0 23.5 + - + +
75R GLU* 4.5 21.1 - - - +
76R HIS 5.5 1.0 - - - +
93T ARG* 5.3 5.1 - - - +
96T GLN* 3.1 50.5 + - - +
97T THR* 3.2 21.5 + - - +
99T VAL* 1.3 75.2 - - - +
101T LEU* 1.3 60.2 + - - +
103T LEU 3.3 14.7 - - - +
108T ALA* 4.2 12.8 - - + +
112T VAL* 3.9 22.7 - - + +
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Residues in contact with LEU 101 (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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69R ASP* 4.2 15.8 - - - +
72R THR* 3.7 25.8 - - + -
73R TYR* 3.5 51.1 - - + +
93R ARG* 2.6 42.6 + - - +
77T GLU* 4.0 14.6 - - - +
81T LEU* 4.2 5.2 - - + -
97T THR* 3.0 34.2 + - + +
98T ALA* 3.6 6.1 - - - +
100T ARG* 1.3 77.5 - - - +
102T LEU* 1.3 57.9 + - - +
103T LEU 4.7 0.4 - - - +
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Residues in contact with LEU 102 (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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93R ARG* 3.8 15.0 - - - +
97S LEU* 3.4 19.2 - - + +
73T ARG* 3.5 29.6 - - + +
74T ILE* 3.5 46.9 - - + +
77T GLU* 3.8 18.4 - - + +
98T ALA 2.8 19.2 + - - +
101T LEU* 1.3 79.0 - - - +
103T LEU* 1.3 73.3 + - + +
104T PRO* 4.0 1.6 - - - +
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Residues in contact with LEU 103 (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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55S VAL* 4.9 4.5 - - + -
59S LEU* 3.7 40.4 - - + -
97S LEU* 4.3 8.7 - - + -
70T ILE* 5.7 1.8 - - + -
74T ILE* 5.3 4.5 - - + -
99T VAL* 2.9 21.0 + - + +
100T ARG 3.3 11.4 - - - +
101T LEU 4.7 0.3 - - - -
102T LEU* 1.3 91.9 - - + +
104T PRO* 1.4 66.7 - - + +
105T GLY 4.1 0.3 + - - -
107T LEU* 3.5 25.1 - - + +
108T ALA* 3.3 28.3 - - - +
111T ALA* 3.6 20.4 - - + -
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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