Contacts of the helix formed by residues 70 - 84 (chain C) in PDB entry 1U1C
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 GLY 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ILE* 1.3 76.7 - - - +
71C GLY* 1.3 60.0 + - - -
72C PRO* 3.5 4.4 - - - -
73C SER* 3.8 2.3 + - - -
74C THR* 2.6 31.3 + - - -
197C MET* 3.2 16.2 - - - -
198C GLU* 3.1 13.7 + - - +
72D PRO* 3.6 20.6 - - - -
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Residues in contact with GLY 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLY* 1.3 70.7 - - - -
72C PRO* 1.3 62.7 - - - +
74C THR* 3.2 3.1 + - - -
75C SER* 2.7 37.6 + - - -
117C ASP* 5.9 0.2 - - - +
119C ALA* 3.9 4.5 - - - -
160C ASP* 4.4 5.4 + - - -
197C MET 3.7 5.8 + - - -
198C GLU* 5.3 0.7 - - - -
201C THR* 3.2 35.4 - - - +
72D PRO* 4.2 2.6 - - - +
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Residues in contact with PRO 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE 5.4 0.2 - - - +
70C GLY 3.5 4.3 - - - -
71C GLY* 1.3 88.5 - - - +
73C SER* 1.3 59.3 + - - +
75C SER* 2.5 21.4 + - - +
76C ILE* 3.3 11.8 + - - +
119C ALA* 4.6 3.1 - - + -
160C ASP* 4.7 1.8 - - - +
69D ILE 4.1 0.9 - - - +
70D GLY* 3.5 30.5 - - - -
72D PRO* 3.8 16.6 - - + -
160D ASP* 3.0 48.4 - - - +
197D MET* 3.8 14.4 - - + +
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 3.4 21.3 + - - -
50C PHE* 3.2 23.7 - - - -
67C THR 2.7 22.2 + - - -
69C ILE 3.8 1.9 + - - -
70C GLY 3.8 6.9 + - - -
71C GLY 3.5 0.2 - - - -
72C PRO* 1.3 77.5 - - - +
74C THR* 1.3 60.6 + - - +
76C ILE* 3.3 3.1 + - - +
77C ALA* 3.0 24.9 + - - +
1003C K 2.9 19.8 - - - -
69D ILE* 4.0 11.5 + - - +
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Residues in contact with THR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C THR* 3.5 30.5 + - + +
68C GLY 3.9 0.9 + - - -
70C GLY 2.6 22.5 + - - -
71C GLY* 3.2 9.4 + - - -
73C SER* 1.3 80.2 + - - +
75C SER* 1.3 56.4 + - - +
77C ALA* 3.4 1.4 + - - +
78C VAL* 3.0 41.0 + - + +
91C ARG* 5.8 1.3 - - - -
198C GLU* 3.3 26.3 - - + +
201C THR* 4.7 1.6 - - + -
202C LEU* 4.2 29.2 - - + +
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Residues in contact with SER 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLY 2.7 16.5 + - - -
72C PRO* 2.5 23.7 + - - +
74C THR* 1.3 71.2 - - - +
76C ILE* 1.3 63.3 + - - +
79C GLU* 3.2 26.5 + - - +
119C ALA* 4.8 1.8 - - - -
123C PHE* 4.0 20.7 - - - -
201C THR* 4.1 3.8 - - - +
205C MET* 3.5 15.9 - - - +
161D THR* 3.1 27.4 + - - -
162D PHE 4.6 0.2 + - - -
163D TYR* 5.0 2.2 - - - -
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Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C HIS* 3.5 39.3 - - + +
9C LEU* 5.1 0.7 - - + -
50C PHE* 3.9 9.9 - - + -
72C PRO 3.6 10.3 - - - +
73C SER* 3.3 9.5 + - - +
75C SER* 1.3 78.5 + - - +
77C ALA* 1.3 65.0 + - - +
79C GLU* 3.9 0.7 - - - +
80C GLU* 3.1 35.4 + - - +
69D ILE* 3.7 40.8 - - + -
162D PHE* 3.7 31.6 - - + +
163D TYR* 4.6 7.4 - - + -
197D MET* 4.1 4.9 - - + -
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 3.9 16.6 - - + +
50C PHE* 3.8 18.4 - - + -
65C CYS* 4.6 6.1 - - - -
66C SER 4.1 3.8 - - - +
67C THR* 4.1 20.2 - - + -
73C SER 3.0 16.3 + - - +
74C THR 3.8 3.6 - - - +
76C ILE* 1.3 77.1 - - - +
78C VAL* 1.3 57.7 + - + +
80C GLU 3.6 0.2 + - - -
81C LEU* 3.0 38.5 + - + +
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Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 5.5 1.3 - - + -
67C THR* 5.0 6.5 - - + -
74C THR* 3.0 28.3 + - + +
77C ALA* 1.3 72.4 - - - +
79C GLU* 1.3 60.5 + - - +
81C LEU 3.4 0.7 + - - -
82C ALA* 2.9 28.2 + - - +
89C PHE* 3.5 36.0 - - + -
202C LEU* 3.7 25.8 - - + -
205C MET* 3.7 26.0 - - + -
206C CYS* 4.1 13.9 - - - -
211C LEU* 4.6 6.5 - - + -
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C SER 3.2 19.8 + - - +
76C ILE 3.9 1.6 - - - +
77C ALA 3.4 0.2 - - - -
78C VAL* 1.3 78.4 - - - +
80C GLU* 1.3 59.7 + - - +
82C ALA* 3.3 5.9 + - - +
83C GLN* 2.8 47.5 + - - +
123C PHE* 5.5 4.8 - - + -
205C MET* 4.0 8.4 - - + +
209C GLN* 4.5 15.0 + - - +
163D TYR* 3.7 30.5 - - + +
171D THR* 3.3 15.3 - - - -
172D TYR* 2.9 31.7 + - - +
173D SER 4.9 0.2 + - - -
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 3.4 21.3 - - + +
7C PHE 3.7 6.1 + - - +
8C HIS* 2.8 48.9 + - - +
9C LEU* 3.1 28.9 + - + +
76C ILE* 3.1 23.1 + - - +
79C GLU* 1.3 75.2 - - - +
81C LEU* 1.3 62.2 + - - +
83C GLN* 3.6 7.2 - - - +
84C LEU* 3.2 27.2 + - - +
163D TYR* 2.7 31.9 + - + +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 3.8 14.1 - - + -
11C LEU* 4.7 10.3 - - + -
16C LEU* 4.8 7.2 - - + -
22C ALA* 4.5 4.7 - - + -
24C VAL* 4.3 11.9 - - + -
63C ILE* 3.9 21.1 - - + -
65C CYS* 3.9 26.9 - - + -
77C ALA* 3.0 25.3 + - + +
78C VAL 3.8 3.6 - - - +
80C GLU* 1.3 74.6 - - - +
82C ALA* 1.3 61.0 + - - +
84C LEU* 3.1 16.1 + - + +
85C GLY 3.1 1.0 + - - -
86C ILE* 3.0 46.0 + - + +
89C PHE* 4.0 17.9 - - + -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C VAL 2.9 18.8 + - - +
79C GLU* 3.3 8.5 + - - +
81C LEU* 1.3 72.1 - - - +
83C GLN* 1.3 63.0 - - - +
85C GLY 3.3 3.1 + - - -
86C ILE 3.5 17.5 - - - +
87C ARG* 2.8 27.7 + - - +
89C PHE* 4.3 1.9 - - + -
211C LEU* 4.2 13.5 - - + -
172D TYR* 3.7 30.8 - - + -
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Residues in contact with GLN 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ASP 4.5 7.1 - - - +
6C VAL* 4.3 15.2 - - + +
13C LYS* 3.9 12.5 - - - +
79C GLU* 2.8 43.6 + - - +
80C GLU* 3.6 14.0 - - - +
81C LEU 3.2 0.2 - - - -
82C ALA* 1.3 76.5 - - - +
84C LEU* 1.3 60.8 + - + +
85C GLY 3.3 0.7 + - - -
87C ARG* 5.6 0.5 + - - -
163D TYR* 4.5 12.9 + - - -
170D ASP 4.0 17.9 + - - +
171D THR* 4.2 1.9 - - - +
172D TYR* 4.2 14.6 - - + +
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ASP* 4.3 8.7 - - + -
6C VAL* 3.9 19.3 - - + -
9C LEU* 4.5 1.6 - - + -
11C LEU* 3.6 38.8 - - + +
12C THR* 3.6 6.3 - - - -
13C LYS* 3.4 52.9 - - + +
16C LEU* 3.6 32.0 - - + +
19C ALA 4.8 0.7 - - - +
80C GLU 3.2 20.0 - - - +
81C LEU* 3.1 15.0 + - + +
83C GLN* 1.3 77.1 - - - +
85C GLY* 1.3 56.5 + - - +
86C ILE 3.7 0.2 - - - -
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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