Contacts of the helix formed by residues 309 - 318 (chain C) in PDB entry 6IY6
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 LEU 309 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268C TRP* 4.2 16.8 - - + -
274C LEU* 3.9 18.6 - - + -
305C SER 3.4 14.1 - - - +
306C CYS* 2.9 20.3 + - - +
307C GLU 3.4 5.4 - - - +
308C ASN* 1.3 81.9 - - + +
310C ALA* 1.3 58.8 + - - +
311C PRO* 4.1 5.8 - - + -
312C PHE* 3.5 32.2 + - + -
313C ASN* 2.9 24.4 + - - -
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Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 4.8 8.3 - - - +
144C GLU* 4.1 11.4 - - - +
308C ASN 3.8 1.4 + - - -
309C LEU* 1.3 69.7 - - - +
311C PRO* 1.4 70.0 - - + +
312C PHE 3.2 0.3 + - - -
313C ASN* 3.2 14.3 - - - +
314C THR* 2.9 33.1 + - + +
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Residues in contact with PRO 311 (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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137C VAL* 4.0 7.7 - - + +
140C ARG* 3.3 31.6 - - + +
141C LEU* 3.7 28.7 - - + -
144C GLU* 3.5 28.3 - - - +
309C LEU* 3.6 11.0 - - + -
310C ALA* 1.4 96.2 - - + +
312C PHE* 1.3 63.8 + - + +
314C THR* 3.0 10.6 + - - -
315C ALA* 3.3 17.0 - - - +
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Residues in contact with PHE 312 (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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137C VAL* 3.9 20.4 - - + -
141C LEU* 4.8 5.2 - - + -
274C LEU* 4.1 15.5 - - + -
279C VAL* 3.7 36.6 - - + -
282C TRP* 3.4 46.6 - + + -
306C CYS* 3.2 48.9 - - + +
307C GLU* 4.3 1.8 - - - -
309C LEU* 3.7 27.8 - - + +
310C ALA 3.2 0.6 - - - -
311C PRO* 1.3 80.4 - - + +
313C ASN* 1.3 61.6 + - - +
315C ALA* 4.0 1.7 - - - +
316C LEU* 3.2 30.1 + - - +
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Residues in contact with ASN 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C TRP* 6.2 0.2 - - - -
307C GLU* 3.5 17.3 + - - +
308C ASN 4.0 5.3 + - - -
309C LEU 2.9 22.4 + - - -
310C ALA* 3.2 16.4 + - - +
312C PHE* 1.3 76.9 - - - +
314C THR* 1.3 85.0 + - - +
316C LEU* 3.2 7.2 + - - +
317C LYS* 2.9 47.3 + - + +
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Residues in contact with THR 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 3.6 26.5 - - - +
310C ALA* 2.9 23.0 + - + +
311C PRO* 3.0 13.2 + - - +
313C ASN* 1.3 90.3 + - - +
315C ALA* 1.3 64.5 + - - -
317C LYS* 3.7 5.8 + - - +
318C LEU* 3.3 35.8 + - - +
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Residues in contact with ALA 315 (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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133C LEU* 4.3 9.3 - - + +
136C LEU* 4.1 16.2 - - + +
137C VAL* 4.0 32.8 - - + +
140C ARG* 5.4 1.8 - - + -
168C CYS 5.9 0.9 - - - -
311C PRO 3.3 17.0 + - - +
312C PHE 4.0 1.1 - - - +
313C ASN 3.3 0.4 - - - -
314C THR* 1.3 79.8 + - - +
316C LEU* 1.3 60.7 + - - +
318C LEU* 3.5 9.2 + - - +
319C LEU* 3.4 19.8 + - - +
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Residues in contact with LEU 316 (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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133C LEU* 4.3 23.3 - - + +
282C TRP* 3.8 25.4 - - + -
286C GLN* 3.9 24.5 - - + +
307C GLU* 4.9 8.1 - - + -
312C PHE 3.2 19.3 + - - +
313C ASN* 3.2 6.7 + - - +
315C ALA* 1.3 73.6 - - - +
317C LYS* 1.3 59.0 + - - +
319C LEU* 3.3 17.9 + - + +
320C LYS* 3.0 29.8 + - + +
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Residues in contact with LYS 317 (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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313C ASN* 2.9 30.4 + - + +
314C THR* 3.9 6.3 - - - +
316C LEU* 1.3 75.9 - - - +
318C LEU* 1.3 59.6 + - + +
319C LEU 3.2 4.5 + - - -
320C LYS* 3.5 23.5 + - - +
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Residues in contact with LEU 318 (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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164C ASN* 3.8 27.2 + - - +
165C LEU* 5.5 0.5 - - - +
167C LYS 4.7 10.5 - - - +
168C CYS* 3.4 33.6 - - - +
169C PHE* 4.6 11.0 - - - +
170C GLY* 5.7 2.7 - - - +
314C THR* 3.3 26.3 + - - +
315C ALA* 3.9 7.6 - - - +
316C LEU 3.4 0.6 - - - -
317C LYS* 1.3 76.2 - - + +
319C LEU* 1.3 56.5 + - - +
320C LYS 4.4 1.3 - - - -
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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