Contacts of the helix formed by residues 277 - 292 (chain I) in PDB entry 1I43
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 PRO 277 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I GLU* 3.7 16.2 - - + +
248I LEU* 5.2 1.3 - - + -
253I ASP* 3.0 21.5 - - + +
254I LEU* 4.5 0.2 - - + -
276I GLY* 1.3 87.1 - - - +
278I LEU* 1.3 58.8 + - - +
279I LYS* 4.5 7.2 - - + +
280I LEU* 3.4 30.1 + - + +
281I VAL* 2.9 27.4 + - - +
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Residues in contact with LEU 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I GLU* 2.9 42.1 + - + +
131I SER* 4.4 11.0 - - - -
277I PRO* 1.3 67.6 - - - +
279I LYS* 1.3 67.9 + - - +
280I LEU 2.9 2.2 + - - -
281I VAL* 3.8 7.2 - - + -
282I SER* 2.9 40.8 + - - -
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Residues in contact with LYS 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I GLU* 4.5 1.4 + - - -
277I PRO* 3.5 5.1 - - + +
278I LEU* 1.3 79.8 - - - +
280I LEU* 1.3 70.9 + - + +
282I SER* 3.5 12.0 + - - -
283I GLU* 3.6 13.9 - - - +
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Residues in contact with LEU 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I LEU* 4.3 18.5 - - + +
232I LEU* 4.1 21.1 - - + -
253I ASP* 4.1 16.2 - - + +
254I LEU* 4.0 31.4 - - + -
277I PRO* 3.4 28.6 + - + +
278I LEU 2.9 1.6 + - - -
279I LYS* 1.3 91.0 - - + +
281I VAL* 1.3 60.8 + - - +
282I SER 3.0 1.6 - - - -
283I GLU* 2.8 32.6 + - + +
284I ILE* 3.4 9.2 + - - +
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Residues in contact with VAL 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I SER* 3.1 39.7 - - - +
133I LEU* 3.9 30.5 - - + +
254I LEU* 4.5 3.9 - - + +
274I ILE* 3.9 22.4 - - + +
276I GLY 4.5 5.2 - - - +
277I PRO 2.9 23.3 + - - +
278I LEU* 3.6 6.1 - - + +
280I LEU* 1.3 73.3 - - - +
282I SER* 1.3 61.9 + - - +
284I ILE* 3.3 12.4 + - + +
285I ARG* 2.9 29.6 + - - +
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Residues in contact with SER 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278I LEU* 2.9 34.2 + - - -
279I LYS* 3.5 8.7 + - - -
281I VAL* 1.3 77.0 - - - +
283I GLU* 1.3 72.2 + - - +
285I ARG* 3.0 13.4 + - - +
286I ASN* 3.0 29.5 + - - +
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Residues in contact with GLU 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I ALA* 4.3 16.6 - - - +
149I LEU* 4.5 15.0 - - + +
279I LYS 3.6 15.7 - - - +
280I LEU* 2.8 16.8 + - + +
282I SER* 1.3 84.6 + - - +
284I ILE* 1.3 59.3 + - - +
286I ASN* 3.3 27.1 + - - +
287I LEU* 3.6 4.5 + - - +
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Residues in contact with ILE 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I LEU* 3.7 19.7 - - + -
135I MET* 4.1 4.5 - - + -
144I VAL* 3.8 20.0 - - + -
145I MET* 4.1 19.5 - - + -
148I ALA* 4.0 8.5 - - + -
149I LEU* 4.1 33.4 - - + -
254I LEU* 4.4 6.3 - - + -
274I ILE* 4.0 26.5 - - + -
280I LEU 4.0 6.3 - - - +
281I VAL* 3.3 18.8 + - + +
282I SER 3.2 0.2 - - - -
283I GLU* 1.3 73.2 - - - +
285I ARG* 1.3 60.7 + - - +
287I LEU* 3.1 5.4 + - - +
288I HIS* 2.8 25.9 + - - +
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Residues in contact with ARG 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I TYR 5.5 2.7 + - - -
117I VAL* 6.0 0.6 - - - +
120I GLU* 2.9 33.1 + - - -
131I SER* 3.4 24.2 + - - -
132I THR 3.5 13.1 + - - -
133I LEU* 3.7 26.3 - - + +
281I VAL* 2.9 16.1 + - - +
282I SER* 3.2 15.2 - - - +
284I ILE* 1.3 78.2 - - - +
286I ASN* 1.3 63.9 + - - +
288I HIS* 3.3 9.4 - - - +
289I HIS* 3.0 51.1 + - + +
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Residues in contact with ASN 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282I SER* 3.0 16.7 + - - +
283I GLU* 3.5 22.7 + - - +
284I ILE 3.1 0.4 - - - -
285I ARG* 1.3 80.4 - - - +
287I LEU* 1.3 64.9 + - - +
289I HIS* 3.2 24.2 + - - +
290I ILE* 3.7 14.2 + - - +
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Residues in contact with LEU 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I VAL* 3.6 13.5 - - + +
147I LEU* 3.7 18.2 - - + +
148I ALA* 3.5 40.6 - - + +
283I GLU 3.6 2.7 + - - +
284I ILE 3.1 7.0 + - - +
286I ASN* 1.3 76.3 - - - +
288I HIS* 1.3 65.2 + - - +
290I ILE* 3.0 25.1 + - + +
291I LEU* 3.0 36.5 + - + +
173K ILE* 4.1 30.3 - - + -
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Residues in contact with HIS 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I ARG* 4.9 6.0 + - - +
133I LEU* 3.8 25.5 - - + +
134I LEU 3.8 11.0 + - - -
135I MET* 3.4 27.8 - - + +
144I VAL* 4.1 14.4 - - + +
284I ILE 2.8 13.8 + - - +
285I ARG* 3.3 12.1 - - - +
287I LEU* 1.3 78.6 - - - +
289I HIS* 1.3 72.4 + + - +
291I LEU* 4.6 3.3 - - - +
292I GLY* 3.0 27.5 + - - -
293I GLY* 3.4 37.9 + - - -
294I ALA* 3.7 9.7 - - - -
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Residues in contact with HIS 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I ARG* 3.0 50.7 + - - -
111I TYR* 3.6 48.3 + + + -
285I ARG* 3.0 44.0 + - + +
286I ASN* 3.5 15.9 + - - +
287I LEU 3.2 0.4 - - - -
288I HIS* 1.3 86.1 - + - +
290I ILE* 1.3 60.2 + - + +
292I GLY 4.3 0.9 - - - -
165K LYS* 4.6 7.1 - - - +
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Residues in contact with ILE 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286I ASN 3.9 14.6 - - - +
287I LEU* 3.0 19.7 + - + +
289I HIS* 1.3 82.2 - - + +
291I LEU* 1.3 65.7 + - + +
292I GLY 3.1 2.3 + - - -
139K MET* 3.4 28.0 - - + +
143K THR* 3.8 1.6 + - - -
165K LYS* 4.3 30.3 - - + +
168K ILE* 4.2 22.7 - - + -
169K PHE* 4.0 36.8 - - + +
172K THR* 5.7 1.8 - - - +
173K ILE* 5.6 4.3 - - + -
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Residues in contact with LEU 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I THR* 5.3 1.8 - - + -
144I VAL* 3.8 28.5 - - + -
147I LEU* 4.3 16.4 - - + -
287I LEU* 3.0 42.7 + - + +
288I HIS* 4.4 3.8 - - - +
290I ILE* 1.3 77.0 - - + +
292I GLY* 1.3 64.8 + - - +
293I GLY* 4.9 2.2 - - - +
140K CYS* 3.2 26.9 - - - +
143K THR* 3.4 33.7 - - + +
147K LEU* 5.1 4.3 - - + -
169K PHE* 4.0 19.7 - - + -
173K ILE* 5.8 0.9 - - + -
291K LEU* 6.6 0.4 - - + -
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Residues in contact with GLY 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I ARG* 3.7 20.9 - - - -
288I HIS 3.0 14.5 + - - -
290I ILE 3.1 4.0 - - - -
291I LEU* 1.3 76.9 - - - +
293I GLY* 1.3 55.8 + - - -
294I ALA 3.2 8.5 + - - -
136K ALA* 3.7 5.4 - - - +
137K SER* 2.9 27.6 + - - -
139K MET* 4.4 0.7 - - - -
140K CYS* 3.3 12.9 - - - +
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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