Contacts of the helix formed by residues 301 - 310 (chain C) in PDB entry 3A5Z
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 VAL 301 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ARG* 4.4 4.0 - - - +
23C MET* 3.8 30.1 - - + -
26C ILE* 4.6 11.0 - - + -
95C LEU* 4.0 8.1 - - + -
113C THR* 3.0 28.0 + - + +
114C MET 3.9 0.4 - - - -
115C LEU* 3.7 37.7 - - + +
299C LEU* 4.1 9.0 - - + -
300C GLY* 1.3 68.6 - - - -
302C ASP* 1.3 60.9 + - - +
304C LEU* 3.0 4.5 + - + +
305C VAL* 2.8 40.2 + - + +
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Residues in contact with ASP 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG* 2.7 41.8 + - - +
109C ASN* 6.4 0.2 - - - -
112C PHE* 3.1 17.0 - - - +
113C THR* 2.9 28.5 + - - +
300C GLY 3.4 1.0 - - - -
301C VAL* 1.3 75.6 - - - +
303C ARG* 1.3 58.0 + - + +
305C VAL* 3.2 2.1 + - - +
306C MET* 2.8 30.5 + - - +
314C LEU* 3.6 26.2 - - + -
317C VAL* 3.8 6.6 - - + +
318C ILE* 3.2 16.7 - - - +
991C KAA 4.6 2.4 - - + +
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Residues in contact with ARG 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C TYR* 2.9 35.8 + - + +
108C HIS* 3.0 34.8 + - - -
243C ILE* 3.5 22.2 - - + +
244C GLU* 2.8 46.7 + - - +
245C LEU* 4.8 4.0 - - + -
300C GLY 3.2 8.6 + - - +
301C VAL 3.2 0.6 - - - -
302C ASP* 1.3 77.7 - - - +
304C LEU* 1.3 61.3 + - - +
306C MET* 3.4 11.2 - - + +
307C LEU* 3.1 30.1 + - - +
314C LEU* 3.9 15.9 - - + -
991C KAA 3.5 37.3 + - - +
31D LYS 5.0 1.8 + - - -
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Residues in contact with LEU 304 (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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22C ILE* 5.1 1.6 - - + -
26C ILE* 4.0 24.7 - - + -
134C LEU* 5.0 5.6 - - + -
135C LEU* 4.1 19.1 - - + -
138C VAL* 4.3 23.1 - - + -
139C LEU* 3.9 27.4 - - + -
245C LEU* 4.8 8.4 - - + +
299C LEU* 3.7 28.0 - - + -
300C GLY 3.1 11.8 + - - +
301C VAL* 3.0 11.3 + - + +
303C ARG* 1.3 77.4 - - - +
305C VAL* 1.3 63.0 + - + +
307C LEU* 3.4 6.5 + - - +
308C ALA* 3.0 23.0 + - - +
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Residues in contact with VAL 305 (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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19C ARG* 4.0 28.7 - - + +
22C ILE* 4.0 34.3 - - + -
23C MET* 5.4 0.2 - - - -
301C VAL* 2.8 40.9 + - + +
302C ASP* 3.6 5.6 - - - +
304C LEU* 1.3 68.9 - - + +
306C MET* 1.3 66.6 + - - +
308C ALA* 3.7 0.3 - - - +
309C LEU* 2.9 45.8 + - + +
317C VAL* 3.9 14.4 - - + -
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Residues in contact with MET 306 (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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107C TYR* 3.3 37.7 - - + -
243C ILE* 4.0 20.0 - - + -
302C ASP 2.8 16.3 + - - +
303C ARG* 3.4 11.7 - - - +
304C LEU 3.2 0.2 - - - -
305C VAL* 1.3 77.8 - - - +
307C LEU* 1.3 68.6 + - + +
309C LEU 3.1 1.9 + - - -
310C GLY 2.8 20.4 + - - -
311C ALA* 3.2 37.1 + - + +
312C GLU* 5.1 0.7 - - - +
313C THR* 3.6 33.2 - - - +
314C LEU* 3.7 11.9 - - - -
317C VAL* 3.8 13.5 - - + -
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Residues in contact with LEU 307 (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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139C LEU* 4.0 11.4 - - + -
240C TYR* 3.9 18.6 - - + +
241C LYS* 3.5 41.5 - - + -
243C ILE* 3.8 17.9 - - + -
245C LEU* 3.5 43.3 - - + -
303C ARG 3.1 15.3 + - - +
304C LEU* 3.8 4.9 - - - +
306C MET* 1.3 81.9 - - + +
308C ALA* 1.3 64.2 + - - +
310C GLY* 3.2 12.2 + - - +
311C ALA 5.5 0.7 - - - -
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Residues in contact with ALA 308 (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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22C ILE* 3.8 21.8 - - + -
138C VAL* 4.5 14.4 - - + +
139C LEU* 3.7 17.9 - - + +
304C LEU 3.0 18.2 + - - +
305C VAL 3.7 4.3 - - - +
307C LEU* 1.3 77.0 - - - +
309C LEU* 1.3 64.4 + - + +
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Residues in contact with LEU 309 (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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15C ASN* 3.8 48.0 + - + +
18C LYS* 3.4 44.5 + - + +
19C ARG 4.8 0.7 - - - +
22C ILE* 4.5 8.3 - - + -
305C VAL* 2.9 39.2 + - + +
306C MET 3.9 1.6 - - - +
308C ALA* 1.3 80.2 - - - +
310C GLY* 1.3 61.9 + - - +
311C ALA* 3.5 6.2 + - + +
317C VAL* 4.4 4.9 - - + -
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Residues in contact with GLY 310 (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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306C MET 2.8 5.6 + - - -
307C LEU* 3.2 11.2 + - - -
308C ALA 3.5 0.2 - - - -
309C LEU* 1.3 79.1 - - - +
311C ALA* 1.3 65.4 + - - +
312C GLU* 3.9 9.2 + - - +
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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