Contacts of the helix formed by residues 87 - 99 (chain Z) in PDB entry 6L49
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 87 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208I T 6.0 0.7 - - - +
-203J G 5.2 9.9 + - - +
44Y GLY* 4.5 10.8 - - - -
46Y GLY 6.1 0.2 - - - +
47Y ALA* 4.1 5.4 - - - -
85Z THR* 3.9 22.2 - - + +
86Z ILE* 1.3 78.4 - - - +
88Z SER* 1.3 65.5 + - - +
89Z ARG* 3.3 12.1 + - - +
90Z GLU* 2.6 35.0 + - - +
91Z ILE* 3.5 18.4 + - - +
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Residues in contact with SER 88 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Y GLY* 3.2 33.6 + - - +
47Y ALA* 4.6 3.7 - - - +
50Y TYR* 4.6 7.5 - - - -
87Z THR* 1.3 74.7 - - - +
89Z ARG* 1.3 60.2 + - - +
91Z ILE* 3.6 6.6 + - - +
92Z GLN* 2.9 35.4 + - - +
115Z VAL* 3.4 23.7 - - - +
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Residues in contact with ARG 89 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X GLU 2.5 31.3 + - - -
75X HIS* 2.6 41.7 + - + +
77X LYS* 3.6 35.8 - - - +
81Z ASN* 4.8 0.2 + - - -
87Z THR* 3.3 11.5 + - - +
88Z SER* 1.3 78.9 - - - +
90Z GLU* 1.3 61.9 + - - +
92Z GLN* 3.5 14.9 - - - +
93Z THR* 2.9 31.6 + - - +
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Residues in contact with GLU 90 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-203J G 5.7 1.0 + - - -
75X HIS* 3.5 31.7 + - + +
74Z ALA* 3.7 21.4 - - + +
77Z LEU* 4.2 0.2 - - - +
78Z ALA* 4.3 19.3 - - + +
81Z ASN* 5.5 2.4 - - - +
83Z ARG* 4.9 11.6 - - - +
85Z THR* 4.2 12.2 - - - +
86Z ILE* 4.2 5.8 - - + -
87Z THR* 2.6 49.9 + - - +
88Z SER 3.3 0.2 - - - -
89Z ARG* 1.3 78.7 + - - +
91Z ILE* 1.3 60.5 + - - +
93Z THR* 3.3 4.3 - - - +
94Z ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 91 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y LEU* 5.2 2.9 - - + -
47Y ALA* 3.7 17.9 - - + -
50Y TYR* 3.5 25.6 - - + -
51Y LEU* 3.8 32.3 - - + -
70Z ILE* 3.7 20.2 - - + +
71Z ALA* 5.1 3.4 - - - -
74Z ALA* 3.7 15.7 - - + -
86Z ILE* 3.7 21.3 - - + -
87Z THR 3.5 16.2 - - - +
88Z SER* 3.6 3.3 + - - +
90Z GLU* 1.3 74.9 - - - +
92Z GLN* 1.3 57.5 + - - +
94Z ALA* 3.3 1.9 + - - +
95Z VAL* 2.9 34.6 + - + +
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Residues in contact with GLN 92 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Y TYR* 3.4 24.8 + - + +
88Z SER* 2.9 23.1 + - - +
89Z ARG* 3.5 15.2 - - - +
91Z ILE* 1.3 77.6 - - - +
93Z THR* 1.3 58.8 + - - +
95Z VAL* 3.2 4.3 + - - +
96Z ARG* 2.9 58.1 + - - +
108Z VAL* 4.2 3.8 - - + -
112Z THR* 3.8 25.6 - - - +
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Residues in contact with THR 93 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71X THR* 3.5 23.0 + - - +
75X HIS* 3.5 41.5 - - + +
77Z LEU* 3.7 9.4 - - + -
89Z ARG* 2.9 22.4 + - - +
90Z GLU 3.3 10.5 - - - +
92Z GLN* 1.3 74.1 - - - +
94Z ALA* 1.3 59.7 + - - +
96Z ARG* 3.7 11.2 - - - +
97Z LEU* 2.9 35.0 + - - +
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Residues in contact with ALA 94 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Z ILE* 3.9 25.3 - - + +
73Z GLU* 3.7 25.9 - - + +
74Z ALA* 3.9 5.4 - - + +
77Z LEU* 4.0 7.9 - - + -
90Z GLU 2.9 17.9 + - - +
91Z ILE 3.6 5.4 - - - +
92Z GLN 3.3 0.2 - - - -
93Z THR* 1.3 76.4 - - - +
95Z VAL* 1.3 59.5 + - - +
97Z LEU* 3.8 1.7 - - - +
98Z LEU* 2.9 32.1 + - - +
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Residues in contact with VAL 95 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Y TYR* 3.6 26.0 - - + +
54Y VAL* 3.8 11.7 - - + -
70Z ILE* 3.9 26.2 - - + -
91Z ILE* 2.9 20.2 + - + +
92Z GLN 3.2 4.2 + - - +
94Z ALA* 1.3 76.3 - - - +
96Z ARG* 1.3 58.1 + - - +
98Z LEU* 4.5 2.0 - - - +
99Z LEU* 3.0 40.5 + - + +
104Z ALA* 3.8 4.1 - - - +
107Z ALA* 3.7 29.4 - - + -
108Z VAL* 4.1 7.2 - - + -
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Residues in contact with ARG 96 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71X THR* 4.8 13.0 - - + +
92Z GLN* 2.9 47.0 + - - +
93Z THR* 3.7 12.3 - - - +
94Z ALA 3.3 0.4 - - - -
95Z VAL* 1.3 78.3 - - - +
97Z LEU* 1.3 59.8 + - - +
99Z LEU 3.7 9.2 - - - +
104Z ALA* 4.3 10.4 - - + +
108Z VAL* 3.6 38.0 - - + +
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Residues in contact with LEU 97 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X ASP* 4.0 28.4 - - + +
71X THR* 3.8 27.6 - - + +
72X TYR* 3.6 31.9 - - + +
92X ARG* 2.4 53.4 + - - +
73Z GLU* 5.1 7.4 - - + +
77Z LEU* 4.0 15.0 - - + -
93Z THR* 2.9 30.7 + - - +
94Z ALA* 4.0 3.6 - - - +
96Z ARG* 1.3 77.7 - - - +
98Z LEU* 1.3 57.7 + - - +
99Z LEU 4.6 0.9 - - - +
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Residues in contact with LEU 98 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X ARG* 4.5 6.8 + - - +
95Y LYS* 5.7 4.5 - - - +
96Y LEU* 3.9 30.2 - - + +
66Z ILE* 5.8 1.3 - - + -
69Z ARG* 4.5 27.1 - - + +
70Z ILE* 3.7 32.8 - - + +
73Z GLU* 5.7 7.0 - - + -
94Z ALA 2.9 18.2 + - - +
95Z VAL* 4.3 1.1 - - - +
97Z LEU* 1.3 79.7 - - - +
99Z LEU* 1.3 68.5 + - + +
100Z PRO* 3.8 3.8 - - - +
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Residues in contact with LEU 99 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Y VAL* 4.7 12.6 - - + -
58Y LEU* 4.8 8.5 - - + -
96Y LEU* 3.8 33.4 - - + -
66Z ILE* 6.0 0.2 - - + -
70Z ILE* 5.3 3.1 - - + -
95Z VAL* 3.0 26.3 + - + +
96Z ARG 3.7 10.2 - - - +
97Z LEU 4.6 0.9 - - - +
98Z LEU* 1.3 84.8 - - + +
100Z PRO* 1.3 70.7 - - + +
103Z LEU* 3.8 28.3 - - + +
104Z ALA* 3.4 18.3 - - + +
107Z ALA* 3.8 28.5 - - + -
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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