Contacts of the helix formed by residues 81 - 99 (chain O) in PDB entry 3TDD
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 MET 81 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O ALA* 4.5 10.8 - - + -
78O TYR* 3.9 0.9 - - - -
80O GLY* 1.3 69.0 - - - -
82O GLY* 1.3 67.9 + - - +
83O PRO* 3.4 7.9 - - + -
84O ASP* 3.1 21.0 + - - +
85O TYR* 3.2 1.2 + - - +
130O ARG* 3.4 28.5 - - - +
133O GLY* 2.8 26.4 + - - +
134O VAL* 3.0 18.8 - - - +
15U PHE* 3.6 26.7 - - - -
19U GLY 5.3 1.3 - - - +
21U LEU* 3.8 19.1 - - + -
124U THR* 4.5 3.1 - - + -
154U ALA 6.1 0.4 - - - +
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Residues in contact with GLY 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O TYR* 3.2 27.3 + - - -
80O GLY 3.3 7.1 + - - -
81O MET* 1.3 69.6 - - - +
83O PRO* 1.3 70.9 - - - +
85O TYR* 2.9 16.5 + - - +
86O ARG* 2.9 14.5 + - - +
156U TYR* 6.0 1.8 - - - -
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Residues in contact with PRO 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81O MET* 3.6 9.0 - - + -
82O GLY* 1.3 88.0 - - - +
84O ASP* 1.3 63.1 + - - +
86O ARG* 3.2 23.5 + - - +
87O VAL* 3.2 11.4 + - - +
121U GLN* 3.6 22.8 - - + +
124U THR* 6.2 0.4 - - + -
154U ALA* 3.4 29.6 - - + +
155U GLY 3.5 22.7 - - - +
156U TYR* 3.7 20.6 - - + +
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Residues in contact with ASP 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81O MET* 3.1 23.5 + - - +
83O PRO* 1.3 76.6 - - - +
85O TYR* 1.3 61.9 + - - +
87O VAL* 3.2 6.2 - - - +
88O LEU* 3.0 27.6 + - - +
130O ARG* 2.8 45.7 + - - -
132O PHE* 3.6 16.6 - - + -
133O GLY 2.9 16.1 + - - +
134O VAL* 3.9 10.3 - - + -
121U GLN* 3.0 22.3 - - - +
124U THR* 4.3 1.0 - - - +
125U GLN* 5.0 0.2 - - - -
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Residues in contact with TYR 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65O SER 4.3 6.3 - - - -
66O LYS 2.8 31.4 + - - -
68O SER* 3.2 20.7 + - - -
76O ALA* 2.9 21.6 + - + +
77O VAL* 4.1 7.9 - - - -
78O TYR* 3.4 44.6 - + + -
81O MET 3.2 2.5 + - - +
82O GLY 2.9 10.2 + - - +
84O ASP* 1.3 77.5 - - - +
86O ARG* 1.3 63.4 + - + +
88O LEU* 3.1 8.2 + - + +
89O VAL* 2.8 55.0 + - + +
134O VAL* 4.0 5.3 - - + +
136O LEU* 3.4 30.3 - - + -
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Residues in contact with ARG 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O GLY 2.9 10.4 + - - +
83O PRO* 3.2 18.0 + - - +
85O TYR* 1.3 83.2 - - + +
87O VAL* 1.3 62.9 + - - +
89O VAL* 3.1 16.3 + - + +
90O ASP* 3.1 15.4 + - - +
114U LYS* 4.2 22.2 - - - +
117U ALA* 3.3 22.9 + - - +
118U ASN* 2.8 31.2 - - - +
121U GLN* 4.4 6.1 - - - +
155U GLY* 2.6 31.1 + - - -
156U TYR* 4.3 2.4 - - - +
157U TYR* 3.6 36.6 + - - +
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Residues in contact with VAL 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O PRO 3.2 8.5 + - - +
84O ASP 3.2 11.9 - - - +
86O ARG* 1.3 75.1 - - - +
88O LEU* 1.3 66.8 + - - +
90O ASP* 3.2 11.2 + - - +
91O LYS* 3.0 39.8 + - - +
132O PHE* 3.9 18.8 - - + -
118U ASN* 3.6 27.8 - - + +
121U GLN* 3.5 35.4 - - + +
122U ILE* 5.9 0.7 - - + -
125U GLN* 5.1 0.9 - - - +
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Residues in contact with LEU 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O ASP 3.0 17.2 + - - +
85O TYR* 3.4 6.5 - - - +
87O VAL* 1.3 78.3 - - - +
89O VAL* 1.3 57.1 + - + +
91O LYS* 3.5 5.3 + - + +
92O SER* 2.8 34.4 + - - +
116O VAL* 4.6 10.1 - - + -
119O ILE* 4.0 21.5 - - + -
120O MET* 4.0 22.2 - - + -
132O PHE* 3.5 41.3 - - + -
134O VAL* 3.7 26.9 - - + -
136O LEU* 4.3 13.7 - - + -
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Residues in contact with VAL 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O SER* 3.8 15.0 - - - +
70O LEU* 3.9 11.4 - - + -
76O ALA* 5.5 0.9 - - + -
85O TYR* 2.8 57.4 + - + +
86O ARG* 3.1 9.6 + - + +
88O LEU* 1.3 76.1 - - + +
90O ASP* 1.3 67.3 + - - +
92O SER* 3.3 6.1 + - - -
93O ARG* 3.0 56.9 + - - +
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Residues in contact with ASP 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ARG 3.1 15.3 + - - +
87O VAL* 3.2 11.1 + - - +
89O VAL* 1.3 78.2 - - - +
91O LYS* 1.3 63.3 + - + +
93O ARG* 3.4 16.5 + - - +
94O LYS* 3.1 23.0 + - - +
114U LYS* 3.2 28.9 + - - -
118U ASN* 3.4 22.5 - - - +
65V LEU* 5.4 0.5 - - - +
69V TYR* 3.6 18.8 - - + +
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Residues in contact with LYS 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O VAL* 3.0 35.9 + - - +
88O LEU* 3.8 8.5 - - + +
90O ASP* 1.3 77.0 - - + +
92O SER* 1.3 58.4 + - - +
94O LYS* 3.3 6.5 + - - +
95O VAL* 2.8 32.9 + - - +
119O ILE* 3.9 35.6 - - + +
132O PHE* 4.8 9.9 - - + -
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Residues in contact with SER 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O LEU* 4.1 22.0 - - - +
88O LEU* 2.8 22.6 + - - +
89O VAL* 3.6 6.5 - - - -
90O ASP 3.2 0.2 - - - -
91O LYS* 1.3 73.5 - - - +
93O ARG* 1.3 64.6 + - - +
95O VAL* 3.2 11.6 - - - +
96O ALA* 3.1 24.4 + - - +
112O LEU* 3.7 5.9 - - - +
116O VAL* 3.1 34.2 - - - +
119O ILE* 5.3 2.5 - - - +
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Residues in contact with ARG 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O SER* 3.7 19.6 + - - +
69O LEU* 2.8 29.8 + - - +
70O LEU* 3.7 27.1 - - + +
89O VAL* 3.0 35.1 + - - +
90O ASP* 3.8 18.9 + - - +
92O SER* 1.3 77.8 - - - +
94O LYS* 1.3 62.4 + - - +
96O ALA* 3.4 6.5 - - - +
97O HIS* 3.2 23.6 + - + -
114U LYS* 4.7 3.6 - - - +
65V LEU* 3.4 14.9 - - + +
68V LEU* 3.3 55.4 + - + +
69V TYR* 4.6 0.6 - - - +
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Residues in contact with LYS 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O ASP 3.1 16.5 + - - +
91O LYS* 3.7 6.5 - - - +
93O ARG* 1.3 73.8 - - - +
95O VAL* 1.3 61.7 + - - +
96O ALA 3.0 1.6 - - - -
97O HIS* 2.8 21.1 + - - +
98O THR* 2.9 34.0 + - + -
102O ARG* 5.7 2.5 - - - +
65V LEU* 3.7 25.3 - - + +
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Residues in contact with VAL 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O LYS 2.8 19.6 + - - +
92O SER* 3.2 18.6 - - - +
94O LYS* 1.3 73.5 - - - +
96O ALA* 1.3 66.1 + - - +
98O THR* 3.4 9.0 - - - +
99O SER* 3.0 43.3 + - - +
100O TYR* 3.9 0.9 + - - +
112O LEU* 3.8 14.1 - - + -
115O GLU* 3.7 32.9 - - + +
116O VAL 5.3 0.7 - - - +
119O ILE* 5.0 13.2 - - + -
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Residues in contact with ALA 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O LEU 4.8 1.1 - - - +
71O THR* 4.1 26.2 - - + -
92O SER 3.1 14.1 + - - +
93O ARG* 3.4 13.9 - - - +
94O LYS 3.0 0.4 - - - -
95O VAL* 1.3 79.1 - - - +
97O HIS* 1.3 63.3 + - + +
100O TYR* 3.3 9.5 - - - +
101O LYS* 3.1 21.9 + - - +
106O TYR* 5.2 1.3 - - + -
107O PRO* 3.7 17.3 - - + +
112O LEU* 4.1 8.7 - - + -
115O GLU* 6.3 0.2 - - - -
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Residues in contact with HIS 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O LEU 5.6 3.4 - - - -
93O ARG 3.2 19.8 + - - -
94O LYS 2.8 8.4 + - - +
96O ALA* 1.3 81.1 - - + +
98O THR* 1.3 66.2 + - - +
99O SER 3.3 0.2 - - - -
100O TYR 3.2 4.2 + - - -
101O LYS* 3.9 23.1 - - + +
102O ARG* 2.9 38.1 + - + +
106O TYR* 4.0 13.0 - + - -
61V SER* 2.8 40.2 + - - +
64V GLU* 3.3 41.9 + - + +
65V LEU* 3.9 16.1 - - + +
68V LEU* 5.6 2.5 - - + -
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Residues in contact with THR 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O ILE* 3.9 14.2 - - - +
94O LYS* 2.9 41.6 + - + +
95O VAL* 3.4 18.0 - - - +
97O HIS* 1.3 75.9 - - + +
99O SER* 1.3 67.7 + - - +
100O TYR 3.7 0.3 + - - -
102O ARG* 3.7 33.5 - - - +
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Residues in contact with SER 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O ILE* 3.9 15.9 - - - +
95O VAL* 3.0 30.6 + - - +
98O THR* 1.3 83.1 + - - +
100O TYR* 1.3 68.5 + - - +
103O TYR* 4.8 2.6 - - - -
115O GLU* 4.1 19.3 + - - +
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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
------------------------------------------------------------
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