Contacts of the helix formed by residues 198 - 214 (chain C) in PDB entry 4IA4
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 ALA 198 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TYR* 3.3 26.5 - - + +
182C ALA* 3.5 15.8 + - + +
197C LEU* 1.3 71.4 - - - +
199C PRO* 1.3 66.3 - - + +
200C LEU 3.4 1.1 - - - -
201C PRO* 3.0 23.3 - - + +
202C ILE* 3.4 16.0 - - - +
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Residues in contact with PRO 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 3.4 40.8 - - + +
89C VAL* 3.7 16.8 - - + +
90C TYR* 3.6 32.8 - - + +
93C ALA* 5.7 1.1 - - + -
197C LEU 3.3 12.2 - - - +
198C ALA* 1.3 81.7 - - - +
200C LEU* 1.3 61.7 + - - +
202C ILE* 3.3 3.3 + - + +
203C GLY* 2.7 29.8 + - - -
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Residues in contact with LEU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 5.0 14.8 - - + -
204A PHE* 5.8 4.9 - - + -
86B PHE* 3.9 25.6 - - + -
200B LEU* 4.9 16.8 - - + -
86C PHE* 3.5 31.2 - - + -
198C ALA 3.4 0.2 - - - -
199C PRO* 1.3 83.7 - - - +
201C PRO* 1.3 72.7 - - + +
203C GLY* 3.0 1.0 + - - -
204C PHE* 2.9 38.5 + - + +
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Residues in contact with PRO 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 4.1 19.5 - - + -
87B VAL* 4.2 5.1 - - + +
90B TYR* 3.5 58.1 - - + +
178C THR* 3.9 12.9 - - + +
198C ALA* 3.0 25.6 - - + +
200C LEU* 1.3 89.2 - - + +
202C ILE* 1.3 56.4 + - + +
204C PHE* 3.2 3.8 + - - +
205C ALA* 2.8 28.6 + - - +
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Residues in contact with ILE 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE* 4.1 15.3 - - + -
89C VAL* 4.6 11.0 - - + -
104C VAL* 6.3 0.4 - - + -
175C LEU* 3.9 19.5 - - + -
178C THR* 4.5 4.0 - - - +
179C VAL* 4.1 23.1 - - + +
182C ALA* 4.1 15.9 - - + -
197C LEU* 3.7 39.3 - - + -
198C ALA 3.4 13.7 - - - +
199C PRO* 3.3 7.2 + - + +
200C LEU 3.2 0.2 - - - -
201C PRO* 1.3 75.1 - - - +
203C GLY* 1.3 64.9 + - - +
205C ALA* 3.1 17.5 + - - +
206C VAL* 3.1 13.9 + - - +
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Residues in contact with GLY 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLY* 3.3 30.9 - - - -
85C ILE* 3.8 10.3 - - - +
86C PHE* 4.0 7.4 - - - -
199C PRO 2.7 18.5 + - - -
200C LEU 3.5 3.6 - - - -
202C ILE* 1.3 72.7 - - - +
204C PHE* 1.3 57.3 + - - +
206C VAL* 3.1 3.8 + - - +
207C PHE* 2.9 23.7 + - - -
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Residues in contact with PHE 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PHE* 5.5 4.7 - + - -
79B TRP* 4.0 31.9 - + - -
83B GLY* 4.1 24.7 - - - -
86B PHE* 3.9 24.7 - + + -
87B VAL* 3.6 14.6 - - + -
200B LEU* 5.6 5.4 - - + -
204B PHE* 5.5 5.2 - + - -
79C TRP* 4.2 23.3 - + - -
200C LEU* 2.9 35.2 + - + +
201C PRO 3.6 4.5 - - - +
203C GLY* 1.3 71.4 - - - +
205C ALA* 1.3 60.4 + - - +
207C PHE* 3.4 12.1 - + - +
208C MET* 2.7 43.4 + - + +
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Residues in contact with ALA 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 4.0 12.9 - - + +
174C VAL* 4.3 6.1 - - + +
175C LEU* 4.2 17.0 - - + -
178C THR* 3.5 26.9 - - - +
201C PRO 2.8 12.6 + - - +
202C ILE* 3.1 11.4 + - - +
204C PHE* 1.3 75.5 - - - +
206C VAL* 1.3 61.9 + - - +
208C MET* 3.8 4.1 - - - +
209C VAL* 3.1 31.6 + - - +
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PHE* 5.6 1.6 - - + -
81C PHE* 3.7 21.1 - - + +
82C GLY* 3.9 2.2 - - - -
85C ILE* 3.8 24.5 - - + -
175C LEU* 3.7 27.6 - - + -
202C ILE 3.1 11.2 + - - +
203C GLY 3.1 8.4 + - - +
205C ALA* 1.3 74.8 - - - +
207C PHE* 1.3 64.1 + - - +
209C VAL* 3.6 0.3 + - - +
210C HIS* 2.7 55.2 + - + +
219C THR* 4.0 1.0 - - - +
221C ILE* 4.8 12.1 - - + -
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Residues in contact with PHE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TRP* 4.2 14.6 - + - -
75C LEU* 3.7 13.7 - - + -
78C ALA* 3.3 39.0 - - + -
79C TRP* 3.3 62.1 - + + -
82C GLY* 3.7 12.5 - - - -
203C GLY 2.9 12.4 + - - +
204C PHE* 3.4 19.1 - + + +
206C VAL* 1.3 76.1 - - - +
208C MET* 1.3 88.8 + - + +
210C HIS* 3.1 12.8 + - - +
211C LEU* 3.2 20.9 + - + +
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Residues in contact with MET 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 4.0 10.3 - - + +
79B TRP* 3.4 14.8 - - + +
80B ALA* 3.9 7.6 - - - +
83B GLY* 3.2 40.2 - - - +
84B MET* 3.3 29.8 - - - -
87B VAL* 4.3 4.3 - - + -
174C VAL* 5.8 0.2 - - + -
204C PHE* 2.7 31.3 + - + +
205C ALA* 3.8 4.5 - - - +
207C PHE* 1.3 112.4 - - + +
209C VAL* 1.3 64.5 + - + +
211C LEU* 2.9 33.4 + - + +
212C ALA 3.3 3.6 + - - -
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 4.2 18.8 - - + -
171C GLY* 3.7 32.8 - - - +
174C VAL* 3.8 19.1 - - + -
175C LEU* 5.0 1.1 - - + +
205C ALA 3.1 17.2 + - - +
206C VAL 4.0 0.4 - - - +
207C PHE 3.4 0.4 - - - -
208C MET* 1.3 76.5 - - + +
210C HIS* 1.3 50.6 + - - +
212C ALA* 3.3 1.6 + - - +
213C THR* 2.7 45.6 + - - +
219C THR* 4.1 2.0 - - + -
221C ILE* 3.4 31.9 - - + -
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Residues in contact with HIS 210 (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 ALA* 4.1 14.1 - - - -
81C PHE* 2.9 59.1 - + + +
206C VAL* 2.7 29.1 + - + +
207C PHE 3.1 9.0 + - - +
209C VAL* 1.3 68.6 - - - +
211C LEU* 1.3 68.4 + - - +
212C ALA 2.9 1.6 - - - -
214C ILE* 2.8 42.3 + - + +
219C THR* 1.9 79.0 + - + +
220C GLY 5.1 0.4 + - - -
221C ILE* 4.4 1.6 - - - +
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Residues in contact with LEU 211 (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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58B THR* 3.3 27.6 + - + +
72B VAL* 4.1 26.4 - - + +
76B GLY 3.5 22.4 - - - +
79B TRP* 4.0 7.0 - - + -
80B ALA* 3.7 18.4 - - + +
75C LEU* 3.5 19.5 - - + -
78C ALA* 3.3 26.7 - - + -
207C PHE* 3.2 13.9 + - + +
208C MET* 2.9 27.0 + - + +
210C HIS* 1.3 79.6 - - - +
212C ALA* 1.3 59.5 + - - +
214C ILE* 5.2 0.2 - - - -
215C PRO* 4.2 10.4 - - - +
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Residues in contact with ALA 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 5.5 3.4 - - + +
54B ILE* 3.5 36.8 - - + +
57B ALA* 4.0 20.5 - - + +
58B THR* 3.4 18.4 - - - +
208C MET 3.3 1.2 + - - -
209C VAL 3.3 5.7 + - - +
210C HIS 2.9 0.4 - - - -
211C LEU* 1.3 82.1 - - - +
213C THR* 1.3 62.1 + - - +
214C ILE 3.7 0.2 - - - -
215C PRO* 3.7 10.7 - - - +
216C ILE* 4.1 11.2 - - - +
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Residues in contact with THR 213 (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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53B TYR* 4.7 5.9 + - - -
54B ILE* 5.8 0.7 - - - +
167C ALA* 4.4 19.8 + - + +
168C GLU* 4.0 16.6 - - - +
171C GLY* 5.1 1.0 - - - -
209C VAL* 2.7 33.8 + - + +
212C ALA* 1.3 76.7 - - - +
214C ILE* 1.3 65.5 + - - +
215C PRO* 3.2 3.6 - - - -
216C ILE* 2.7 31.4 + - + +
217C THR* 4.6 1.1 - - - +
218C GLY 2.5 39.4 - - - +
219C THR* 4.1 7.0 - - - -
220C GLY 4.7 0.4 - - - +
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Residues in contact with ILE 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 5.4 2.0 - - + -
74C LEU* 4.3 33.0 - - + +
77C ILE* 4.3 26.9 - - + -
78C ALA* 4.3 10.3 - - + +
156C ALA* 5.7 0.3 - - - +
210C HIS* 2.8 43.6 + - + +
211C LEU* 5.4 1.1 - - - -
213C THR* 1.3 70.9 - - - +
215C PRO* 1.3 71.3 - - + +
216C ILE 3.0 1.4 + - - -
217C THR 3.8 1.2 + - - -
218C GLY* 3.2 26.0 + - - -
219C THR* 3.2 14.8 + - - +
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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
------------------------------------------------------------
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