Contacts of the helix formed by residues 198 - 208 (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 GLU 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C GLY* 3.6 3.3 - - - -
67C THR* 4.0 1.9 + - - +
68C GLY 3.2 18.8 - - - +
69C ILE* 3.4 6.6 - - - +
70C GLY 3.1 21.6 + - - +
71C GLY* 4.9 1.6 - - - +
74C THR* 3.3 28.2 - - + +
91C ARG* 2.8 43.7 + - - +
158C SER* 3.5 1.3 + - - -
196C GLU* 3.2 1.6 + - - -
197C MET* 1.3 98.5 + - - +
199C SER* 1.3 65.6 + - - +
200C ALA 3.5 2.6 + - - -
201C THR* 3.6 7.0 + - - -
202C LEU* 3.3 21.5 + - - +
3022C PO4 2.9 20.5 + - - -
5021C BAU 4.9 0.2 - - - +
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Residues in contact with SER 199 (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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91C ARG* 3.9 6.0 - - - +
110C THR* 5.1 0.2 - - - -
113C SER* 2.7 26.8 + - - -
156C THR* 4.1 4.4 - - - +
158C SER* 3.4 3.1 - - - -
196C GLU* 2.6 33.2 + - - -
198C GLU* 1.3 74.5 - - - +
200C ALA* 1.3 58.2 + - - +
202C LEU* 3.3 3.1 + - - -
203C LEU* 2.8 43.1 + - - +
215C MET* 3.8 24.2 - - - -
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Residues in contact with ALA 200 (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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113C SER* 4.0 9.9 - - - -
114C VAL 4.1 0.9 - - - +
115C ARG* 4.0 20.2 - - + -
117C ASP* 3.5 26.9 - - - +
120C SER* 3.7 0.7 - - - -
130C ALA* 3.9 3.5 - - - +
158C SER* 3.1 23.5 + - - +
199C SER* 1.3 79.3 + - - +
201C THR* 1.3 61.1 + - - +
204C THR* 2.7 32.2 + - - -
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Residues in contact with THR 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLY* 3.2 44.4 - - - +
74C THR* 4.7 2.7 - - - -
75C SER* 4.1 12.6 - - - +
117C ASP* 2.6 24.5 + - - +
119C ALA* 3.6 16.7 - - + +
120C SER* 4.1 7.0 - - - +
123C PHE* 4.8 2.0 - - + -
198C GLU* 3.6 7.4 + - - -
199C SER 3.3 0.6 - - - -
200C ALA* 1.3 74.9 - - - +
202C LEU* 1.3 66.0 + - - +
204C THR* 4.0 0.5 - - - -
205C MET* 3.0 34.4 + - - +
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Residues in contact with LEU 202 (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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24C VAL* 4.2 12.1 - - + -
74C THR* 4.2 10.7 - - + +
78C VAL* 3.7 26.0 - - + -
89C PHE* 4.0 21.8 - - + -
91C ARG* 3.7 32.8 - - + +
198C GLU 3.3 13.9 + - - +
199C SER* 3.3 3.7 + - - +
201C THR* 1.3 80.6 - - - +
203C LEU* 1.3 80.9 + - + +
205C MET* 3.6 8.6 - - - +
206C CYS* 3.1 33.5 + - - +
213C ALA* 4.3 7.4 - - + -
214C GLY 4.1 7.4 - - - +
215C MET* 5.1 1.1 - - + -
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Residues in contact with LEU 203 (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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110C THR* 4.2 14.1 - - + -
112C ALA* 4.3 0.9 - - - -
113C SER* 3.7 18.6 - - - +
130C ALA* 3.3 31.6 - - + +
131C VAL 3.6 4.3 - - - +
132C ALA* 3.8 33.7 - - + +
199C SER* 2.8 26.8 + - - +
202C LEU* 1.3 83.5 - - + +
204C THR* 1.3 56.7 + - - +
206C CYS* 4.1 0.7 - - - +
207C ALA* 3.1 32.2 + - - +
213C ALA* 3.8 26.0 - - + +
215C MET* 4.5 9.0 - - + -
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Residues in contact with THR 204 (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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115C ARG* 3.8 13.3 + - - +
120C SER* 3.6 36.2 - - - +
123C PHE* 4.7 1.3 - - + -
124C ALA* 3.9 21.3 - - + +
128C PHE* 4.2 6.4 - - + -
129C PRO 4.8 1.1 - - - -
130C ALA* 3.3 21.1 - - - +
200C ALA 2.7 24.2 + - - -
201C THR 4.0 0.4 - - - -
203C LEU* 1.3 75.0 - - - +
205C MET* 1.3 60.1 + - - +
207C ALA* 3.4 3.2 + - - +
208C SER* 2.9 34.0 + - - -
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Residues in contact with MET 205 (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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74C THR 4.5 0.2 - - - +
75C SER* 3.5 43.7 - - - +
78C VAL* 3.7 33.9 - - + -
79C GLU* 4.0 9.9 - - + +
123C PHE* 3.6 44.4 - - + -
201C THR* 3.0 26.2 + - - +
202C LEU* 3.6 8.3 - - - +
204C THR* 1.3 77.5 - - - +
206C CYS* 1.3 59.6 + - - +
208C SER* 3.9 5.8 - - - -
209C GLN* 2.8 43.6 + - - +
211C LEU* 5.2 0.2 - - - -
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Residues in contact with CYS 206 (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* 4.1 16.6 - - - -
89C PHE* 3.8 30.1 - - - -
202C LEU* 3.1 27.2 + - - +
203C LEU 4.1 0.9 - - - +
205C MET* 1.3 76.0 - - - +
207C ALA* 1.3 64.0 + - - +
208C SER 3.2 1.6 - - - -
209C GLN 3.2 0.2 + - - -
210C GLY* 3.1 6.2 + - - -
211C LEU* 2.8 51.9 + - + +
212C ARG 4.6 0.2 - - - -
213C ALA* 3.7 21.8 - - + -
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Residues in contact with ALA 207 (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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155A VAL* 5.0 6.3 - - + +
190A MET 3.1 13.2 - - - +
191A GLY* 5.0 1.6 - - - -
128C PHE* 3.8 21.5 - - + -
129C PRO 4.8 0.4 - - - +
131C VAL* 3.7 25.8 - - + +
203C LEU 3.1 20.8 + - - +
206C CYS* 1.3 75.8 - - - +
208C SER* 1.3 57.2 + - - +
209C GLN 3.4 0.6 + - - -
210C GLY* 4.4 4.4 + - - -
211C LEU 3.9 3.8 + - - -
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Residues in contact with SER 208 (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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189A ALA 3.7 3.8 - - - +
190A MET* 3.3 38.0 - - - -
123C PHE* 3.8 7.6 + - - +
124C ALA* 4.3 7.1 - - - +
128C PHE* 3.8 13.5 - - - -
204C THR 2.9 24.3 + - - -
205C MET* 3.9 6.9 + - - -
207C ALA* 1.3 77.1 - - - +
209C GLN* 1.3 57.1 + - - +
210C GLY 3.8 0.4 - - - -
175D ARG* 2.9 33.3 + - - -
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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