Contacts of the helix formed by residues 312 - 323 (chain D) in PDB entry 5MKV
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 THR 312 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A ASP* 6.1 0.4 - - - +
312A THR* 5.4 11.9 - - + -
258D LYS* 2.9 25.2 + - - +
310D ASP* 2.7 21.9 + - - +
311D PRO* 1.3 82.9 - - + +
313D THR* 1.3 64.4 + - - +
314D PRO 3.5 0.9 - - - -
315D ASP* 3.5 11.6 + - - +
316D PHE* 3.2 20.6 + - - +
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Residues in contact with THR 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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229D GLU* 5.2 0.3 + - - -
256D MET 3.5 25.1 - - - +
258D LYS* 4.0 28.0 + - + +
282D SER* 4.6 2.7 - - - +
285D THR 5.6 0.7 - - - +
286D ASP* 5.8 0.2 - - - -
308D SER* 3.1 21.6 + - - -
310D ASP* 2.7 27.3 + - - +
312D THR* 1.3 78.6 + - - +
314D PRO* 1.3 69.9 - - + +
316D PHE* 3.2 3.1 + - - +
317D LEU* 2.9 34.8 + - + +
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Residues in contact with PRO 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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282D SER 3.5 14.6 - - - +
283D LEU 3.5 19.7 - - - +
284D GLY 4.3 1.3 - - - +
285D THR* 3.4 35.4 - - - +
286D ASP* 4.8 2.0 - - + +
310D ASP 4.3 1.1 - - - +
311D PRO* 3.6 17.3 - - + +
312D THR 3.8 0.2 - - - -
313D THR* 1.3 93.5 - - - +
315D ASP* 1.3 62.0 + - - +
317D LEU* 3.8 0.8 - - + +
318D ASN* 2.9 32.1 + - - -
368D LYS* 4.1 15.0 - - - +
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Residues in contact with ASP 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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311D PRO 5.7 2.0 - - - -
312D THR* 3.5 12.9 + - - +
313D THR 3.3 0.4 - - - -
314D PRO* 1.3 79.0 - - - +
316D PHE* 1.3 61.9 + - - +
318D ASN* 3.4 1.7 + - - -
319D SER* 3.1 13.0 + - - -
368D LYS* 3.5 27.1 + - - +
372D THR* 6.0 1.7 - - - +
374D LYS* 2.9 33.4 + - - +
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Residues in contact with PHE 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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269C LYS* 5.0 6.7 - - + -
258D LYS* 3.6 63.0 - - + -
261D ALA* 4.2 1.8 - - + -
262D GLU* 4.0 18.4 - - + -
312D THR 3.2 5.3 + - - +
313D THR 3.2 7.6 + - - +
315D ASP* 1.3 77.7 - - - +
317D LEU* 1.3 69.1 + - + +
319D SER* 3.1 9.4 + - - -
320D LEU* 3.0 60.6 + - + +
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Residues in contact with LEU 317 (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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255D VAL* 3.8 12.3 - - + +
256D MET 4.1 2.9 - - - +
257D SER 3.8 14.4 - - - +
258D LYS 4.6 0.2 - - - +
261D ALA* 3.6 31.4 - - + -
278D PRO* 4.7 2.7 - - + -
282D SER* 3.6 45.1 - - - +
283D LEU* 3.9 14.8 - - + +
313D THR* 2.9 27.9 + - + +
314D PRO 3.9 2.0 - - - +
316D PHE* 1.3 80.4 - - + +
318D ASN* 1.3 56.6 + - - +
320D LEU* 3.3 1.5 + - - -
321D LEU* 2.9 30.3 + - - +
326D LEU* 3.9 15.6 - - + +
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Residues in contact with ASN 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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283D LEU* 3.0 43.5 + - - +
314D PRO 2.9 29.5 + - - +
315D ASP* 3.9 4.0 - - - +
317D LEU* 1.3 77.5 - - - +
319D SER* 1.3 58.2 + - - +
321D LEU* 3.5 10.7 + - - +
322D SER* 2.8 29.6 + - - -
365D ILE* 4.5 6.1 - - - -
368D LYS* 3.4 35.2 - - - +
369D ALA* 3.7 18.1 - - + +
374D LYS* 4.2 6.5 - - + +
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Residues in contact with SER 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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268C ARG 5.1 0.5 - - - +
269C LYS 3.7 19.2 - - - +
270C LYS* 5.0 8.0 + - - -
271C GLY* 5.5 3.5 + - - -
601C EDO 5.2 0.3 + - - -
315D ASP 3.1 7.4 + - - -
316D PHE* 3.1 14.0 + - - -
318D ASN* 1.3 76.6 - - - +
320D LEU* 1.3 60.6 + - - +
322D SER* 3.2 6.5 + - - -
323D CYS* 3.1 27.5 + - - +
374D LYS* 3.1 31.7 + - - +
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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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269C LYS* 3.6 28.5 - - + +
261D ALA* 3.7 29.8 - - + +
262D GLU* 4.3 2.2 - - - +
265D ALA* 4.4 7.2 - - + -
316D PHE* 3.0 56.0 + - + +
317D LEU* 4.0 3.4 - - - +
319D SER* 1.3 75.8 - - - +
321D LEU* 1.3 65.7 + - - +
322D SER 3.2 0.4 - - - -
323D CYS* 3.5 3.8 + - - -
324D GLY 3.2 3.5 + - - -
325D ASP* 3.0 49.5 + - + +
326D LEU* 3.1 13.7 + - + -
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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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278D PRO* 4.3 4.0 - - + -
283D LEU* 4.2 19.7 - - + -
317D LEU 2.9 16.5 + - - +
318D ASN* 3.7 12.1 - - - +
320D LEU* 1.3 75.6 - - - +
322D SER* 1.3 62.0 + - - +
324D GLY* 3.5 9.0 + - - -
326D LEU* 3.4 41.8 - - + +
327D GLN 4.1 4.9 - - - +
329D THR* 3.7 29.8 - - + -
365D ILE* 4.5 5.4 - - + -
375D MET* 4.0 9.6 - - + -
383D VAL* 3.7 44.0 - - + +
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Residues in contact with SER 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C EDO 3.8 10.9 + - - -
318D ASN 2.8 21.9 + - - -
319D SER* 3.2 7.1 + - - -
321D LEU* 1.3 79.6 - - - +
323D CYS* 1.3 59.7 + - - +
324D GLY 3.7 0.3 + - - -
369D ALA* 4.2 0.9 - - - +
374D LYS* 3.3 41.3 - - - +
375D MET* 3.3 23.2 - - - +
379D GLN* 3.1 21.9 - - - +
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Residues in contact with CYS 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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268C ARG* 3.3 57.5 + - - +
269C LYS* 3.9 18.8 - - - -
323C CYS 5.7 0.9 - - - +
601C EDO 3.9 7.6 + - - +
268D ARG* 5.5 1.0 + - - -
319D SER 3.1 17.2 + - - +
320D LEU* 3.7 13.0 - - - -
322D SER* 1.3 76.5 - - - +
324D GLY* 1.3 57.5 + - - +
325D ASP* 3.4 26.6 + - - -
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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