Contacts of the helix formed by residues 317 - 328 (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 LYS 317 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313D SER* 2.5 47.3 + - - +
314D ARG* 3.0 16.2 + - - +
316D VAL* 1.3 85.5 - - + +
318D TYR* 1.3 59.1 + - - +
319D PRO 3.3 1.1 - - - -
320D LEU* 3.0 15.9 + - + +
321D LEU* 2.8 38.0 + - + +
38E VAL* 3.8 28.7 - - + -
39E PHE 3.4 29.2 + - - +
40E GLU* 2.7 23.1 + - + +
59E ASP* 5.8 4.9 + - - +
61E ALA* 4.9 5.2 - - - +
63E GLN* 6.2 0.4 - - - +
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Residues in contact with TYR 318 (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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182D MET* 4.8 13.5 - - + -
186D GLU* 2.4 38.8 + - - -
229D HIS* 3.6 11.6 + + - -
253D LEU* 6.0 0.2 - - + -
256D TRP* 3.4 26.6 - + - -
257D LEU* 4.4 9.4 - - + -
260D LEU* 3.6 29.6 - - + -
314D ARG* 3.4 37.5 + - + +
315D LEU* 3.4 25.0 + - + +
317D LYS* 1.3 76.9 - - - +
319D PRO* 1.4 69.9 - - + +
321D LEU* 3.3 11.8 + - + -
322D LEU* 2.9 32.3 + - + +
346D ILE* 3.9 12.6 - - + -
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Residues in contact with PRO 319 (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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315D LEU 3.6 7.9 - - - +
316D VAL 3.6 15.7 - - - +
318D TYR* 1.4 93.0 - - + +
320D LEU* 1.3 58.2 - - + +
322D LEU* 3.8 4.6 - - + +
323D LYS* 3.0 52.7 + - - +
343D ILE* 4.8 3.7 - - + +
346D ILE* 3.7 21.5 - - + -
347D GLN* 5.0 8.7 - - + +
350D LEU* 3.6 22.2 - - + -
66E TYR* 5.0 4.5 - - + +
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Residues in contact with LEU 320 (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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316D VAL 4.1 11.4 - - - +
317D LYS* 3.0 13.4 + - + +
319D PRO* 1.3 76.9 - - + +
321D LEU* 1.3 65.5 + - - +
323D LYS* 3.5 18.8 + - + +
324D GLU* 3.2 22.0 + - - +
19E THR* 5.7 0.2 - - - +
37E THR* 3.9 14.7 - - + +
38E VAL* 4.4 15.0 - - + -
61E ALA* 4.0 18.4 - - + +
62E GLY* 4.0 29.2 - - - +
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Residues in contact with LEU 321 (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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178D ALA* 4.8 3.3 - - - +
181D GLU* 4.0 23.6 - - + +
182D MET* 4.1 28.5 - - + +
314D ARG* 3.5 37.7 - - - +
317D LYS* 2.8 26.3 + - + +
318D TYR* 3.7 10.5 - - + +
320D LEU* 1.3 76.4 - - - +
322D LEU* 1.3 63.0 + - - +
324D GLU* 3.4 7.1 + - + +
325D ILE* 3.2 27.0 + - - +
37E THR* 4.8 2.5 - - - -
38E VAL* 3.7 30.3 - - + -
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Residues in contact with LEU 322 (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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182D MET* 4.0 18.8 - - - -
253D LEU* 3.9 31.0 - - + -
257D LEU* 3.6 29.6 - - + -
318D TYR* 2.9 27.2 + - + +
319D PRO 3.8 3.4 - - - +
321D LEU* 1.3 76.2 - - + +
323D LYS* 1.3 59.4 - - - +
325D ILE* 3.2 8.6 + - + +
326D LEU* 2.9 28.7 + - - +
339D LEU* 4.4 12.2 - - + +
342D ALA* 3.8 22.4 - - + +
343D ILE* 3.9 16.8 - - + +
346D ILE* 4.3 6.7 - - + -
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Residues in contact with LYS 323 (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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319D PRO* 3.0 34.8 + - - +
320D LEU* 3.9 17.3 - - + +
322D LEU* 1.3 76.0 - - - +
324D GLU* 1.3 57.3 + - - +
326D LEU* 3.6 10.6 - - + +
327D LYS* 2.9 28.4 + - - +
343D ILE* 3.7 35.0 - - + -
347D GLN* 4.3 12.5 - - - +
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Residues in contact with GLU 324 (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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178D ALA* 3.7 14.4 - - + -
181D GLU* 5.1 0.4 - - - +
320D LEU 3.2 14.1 + - - +
321D LEU* 3.6 9.6 - - - +
322D LEU 3.2 0.6 - - - -
323D LYS* 1.3 74.8 - - - +
325D ILE* 1.3 65.2 + - - +
327D LYS* 3.2 22.9 + - - +
328D HIS* 2.5 56.2 + - - +
35E VAL 5.7 0.3 - - - +
37E THR* 3.2 34.8 + - + +
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Residues in contact with ILE 325 (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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175D ARG* 3.9 15.1 - - + +
178D ALA* 3.5 25.8 - - + +
179D ILE* 4.0 30.7 - - + -
182D MET* 4.0 30.7 - - + -
249D ILE* 4.3 14.1 - - + -
253D LEU* 4.8 4.0 - - + -
321D LEU 3.2 16.6 - - - +
322D LEU* 3.2 10.2 + - - +
324D GLU* 1.3 76.0 - - - +
326D LEU* 1.3 56.6 + - - +
328D HIS* 3.3 10.5 + - - -
329D THR* 2.7 24.9 + - - +
339D LEU* 3.7 17.0 - - + -
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Residues in contact with LEU 326 (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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171D ARG* 5.1 0.5 + - - -
322D LEU 2.9 16.3 + - - +
323D LYS* 3.6 8.7 - - + +
325D ILE* 1.3 73.2 - - - +
327D LYS* 1.3 65.1 + - - +
329D THR* 3.1 17.8 + - - +
331D LYS* 3.9 23.0 + - - +
336D VAL* 3.6 36.8 - - + +
339D LEU* 3.7 19.2 - - + +
340D GLU* 4.0 22.4 - - + +
343D ILE* 4.0 18.8 - - + -
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Residues in contact with LYS 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ARG* 3.4 20.1 + - - -
174D ARG* 4.2 8.9 + - - +
323D LYS 2.9 17.7 + - - +
324D GLU* 3.2 20.8 + - - +
326D LEU* 1.3 76.9 - - - +
328D HIS* 1.3 76.3 + - + +
329D THR 3.4 0.2 - - - -
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Residues in contact with HIS 328 (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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171D ARG* 3.5 37.5 - - + +
172D GLU* 4.9 0.9 + - - +
174D ARG* 2.8 68.6 + - + +
175D ARG* 3.5 23.6 - - + +
178D ALA* 4.2 1.1 - - + -
324D GLU* 2.5 54.9 + - + +
325D ILE* 3.3 5.1 + - - +
326D LEU 3.1 0.4 - - - -
327D LYS* 1.3 91.4 - - + +
329D THR* 1.3 60.0 + - - +
330D PRO* 3.6 5.7 - - - +
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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