Contacts of the helix formed by residues 309 - 316 (chain D) in PDB entry 4XH9
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 ASP 309 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270D GLN* 2.7 24.1 + - - +
305D TRP* 2.9 21.1 + - + +
306D SER 3.2 6.7 + - - +
307D PHE 3.2 0.6 - - - -
308D LEU* 1.3 76.4 - - - +
310D ILE* 1.3 63.6 + - - +
311D PRO 3.4 2.9 - - - -
312D ARG* 2.6 51.1 + - - +
313D SER* 3.0 27.3 + - - -
41E ASN* 5.1 1.2 + - - +
58E TRP* 3.5 22.2 - - + -
72E LEU* 4.8 0.4 - - - +
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Residues in contact with ILE 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D LEU* 3.4 36.6 - - + +
192D ASP* 4.8 22.0 - - + +
193D LEU* 3.9 11.0 - - + -
300D ARG* 6.1 0.4 - - - +
302D LEU* 6.4 1.8 - - + -
306D SER* 3.4 17.0 + - - +
307D PHE* 3.1 31.4 - - + +
309D ASP* 1.3 78.1 - - - +
311D PRO* 1.4 67.5 - - + +
313D SER* 3.8 3.2 - - - -
314D ARG* 2.9 24.6 + - + +
40E GLU* 4.8 17.3 - - + +
41E ASN* 6.1 2.7 - - + +
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Residues in contact with PRO 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D LEU* 5.4 2.5 - - + -
193D LEU* 4.7 4.5 - - + -
222D LEU* 3.6 31.0 - - + +
263D TYR* 3.7 39.0 - - + -
266D TYR* 3.7 18.4 - - + -
267D CYS* 4.6 3.8 - - - -
308D LEU 3.6 7.9 - - - +
309D ASP 3.6 0.7 - - - -
310D ILE* 1.4 94.5 - - + +
312D ARG* 1.3 56.5 + - - +
314D ARG* 3.2 4.5 + - + +
315D LEU* 2.9 37.7 + - + +
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Residues in contact with ARG 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D CYS* 4.3 9.3 - - - -
270D GLN* 3.9 10.7 + - - +
309D ASP* 2.6 47.2 + - - +
310D ILE 3.4 0.2 - - - -
311D PRO* 1.3 79.5 - - - +
313D SER* 1.3 62.6 + - - +
315D LEU* 3.5 10.6 + - - +
316D VAL* 3.4 28.5 + - + +
58E TRP* 4.7 2.2 - - - -
63E GLN* 3.1 34.0 + - - +
69E LEU* 2.9 47.1 + - + +
70E ARG 3.7 2.0 + - - -
72E LEU* 3.7 32.2 - - - +
73E SER* 2.7 31.7 + - - +
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Residues in contact with SER 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D ASP* 3.0 29.2 + - - -
310D ILE* 3.8 5.4 - - - -
312D ARG* 1.3 79.5 - - - +
314D ARG* 1.3 57.8 + - - +
316D VAL* 3.4 10.6 - - - +
317D LYS* 2.5 52.6 + - - +
40E GLU* 2.8 16.7 + - - -
41E ASN* 4.8 8.6 + - - -
59E ASP 5.7 1.4 + - - -
63E GLN* 5.3 6.4 + - - +
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Residues in contact with ARG 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D GLU 5.1 0.6 + - - -
182D MET* 2.9 26.7 + - - +
185D GLY* 3.6 25.6 + - - -
186D GLU* 2.7 31.3 + - - +
189D LEU* 3.7 28.9 - - + +
229D HIS* 5.4 0.2 - - + -
310D ILE* 2.9 19.7 + - + +
311D PRO* 3.8 4.0 - - + +
313D SER* 1.3 75.6 - - - +
315D LEU* 1.3 67.8 + - + +
317D LYS* 3.0 24.2 + - - +
318D TYR* 3.4 23.5 + - + +
321D LEU* 3.5 30.8 - - - +
38E VAL* 4.9 10.1 - - - +
40E GLU* 3.9 13.9 + - - +
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 3.9 44.2 - - + -
263D TYR* 3.9 24.2 - - + -
267D CYS* 3.9 11.2 - - - -
311D PRO* 2.9 30.4 + - + +
312D ARG* 3.8 6.1 - - - +
313D SER 3.4 0.2 - - - -
314D ARG* 1.3 77.6 - - + +
316D VAL* 1.3 61.0 + - + +
317D LYS 3.2 1.2 + - - -
318D TYR* 3.4 21.2 + - + +
319D PRO* 3.6 7.1 - - - +
346D ILE* 4.5 2.8 - - + +
350D LEU* 3.7 22.2 - - + +
353D ILE* 3.9 28.3 - - + -
69E LEU* 6.4 1.3 - - + -
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Residues in contact with VAL 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ARG* 3.5 16.8 - - + +
313D SER* 3.4 20.2 - - - +
315D LEU* 1.3 75.6 - - + +
317D LYS* 1.3 61.6 + - + +
319D PRO* 3.6 10.8 - - - +
320D LEU* 4.1 4.5 - - - +
350D LEU* 4.1 18.6 - - + +
61E ALA 3.9 15.7 - - - +
62E GLY* 3.6 35.3 - - - +
63E GLN* 4.0 22.2 - - + +
66E TYR* 4.6 9.9 - - + -
69E LEU* 4.7 14.4 - - + -
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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