Contacts of the helix formed by residues 309 - 324 (chain A) in PDB entry 3K57
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 ASN 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A ILE 3.5 4.6 + - - -
308A ASP* 1.3 77.6 - - - +
310A PRO* 1.3 77.2 - - - +
311A TRP* 3.2 4.5 - - - +
312A ASP* 3.4 10.9 + - - +
313A ARG* 3.1 18.1 + - - +
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Residues in contact with PRO 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ASP 4.8 0.2 - - - +
309A ASN* 1.3 81.8 - - - +
311A TRP* 1.3 69.9 + - + +
313A ARG* 3.3 7.5 + - + +
314A MET* 2.8 35.6 + - - +
721A GLN* 5.7 6.7 - - - +
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Residues in contact with TRP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ARG* 4.9 16.8 - - - -
309A ASN* 3.2 1.9 - - - -
310A PRO* 1.3 90.8 - - + +
312A ASP* 1.3 73.3 + - - +
314A MET* 3.4 6.3 + - + +
315A ASP* 3.0 33.7 + - - +
713A ASN* 5.7 0.4 - - - -
718A ARG* 3.6 47.8 - - + +
719A PRO* 3.4 31.4 - - + -
721A GLN* 5.5 9.4 - - - +
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Residues in contact with ASP 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ASP* 4.3 17.3 - - - +
309A ASN* 3.4 15.7 + - - +
311A TRP* 1.3 81.5 - - - +
313A ARG* 1.3 56.8 + - - +
315A ASP* 3.4 8.7 + - - +
316A GLU* 2.8 30.9 + - - +
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A SER* 3.6 30.5 + - - -
308A ASP* 3.5 25.4 + - + +
309A ASN 3.1 18.2 + - - +
310A PRO* 3.4 8.3 - - + +
312A ASP* 1.3 75.6 - - - +
314A MET* 1.3 64.6 + - - +
316A GLU* 3.2 13.0 + - - +
317A ILE* 3.0 35.4 + - + +
320A ARG* 5.1 6.1 - - - +
331A TYR* 3.3 48.6 + - - +
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Residues in contact with MET 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A THR* 4.1 14.8 - - - +
160A THR 3.8 4.3 - - - +
161A ARG* 3.1 67.3 - - + +
310A PRO 2.8 18.0 + - - +
311A TRP* 3.8 8.7 - - + +
312A ASP 3.3 0.2 - - - -
313A ARG* 1.3 77.9 - - - +
315A ASP* 1.3 60.7 + - - +
317A ILE* 3.4 12.0 + - - +
318A ASP* 3.1 30.6 + - - +
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Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG* 2.9 26.5 + - - -
311A TRP* 3.0 26.9 + - - +
312A ASP* 3.8 8.3 - - - +
314A MET* 1.3 72.6 - - - +
316A GLU* 1.3 60.5 + - - +
318A ASP* 3.2 7.4 + - - +
319A ARG* 2.8 30.9 + - - +
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Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ASP* 4.7 9.6 - - - +
312A ASP 2.8 18.8 + - - +
313A ARG* 3.2 16.4 + - - +
315A ASP* 1.3 77.0 - - - +
317A ILE* 1.3 55.6 + - + +
319A ARG* 2.5 48.9 + - - -
320A ARG* 2.9 64.7 + - - +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLU* 3.7 22.0 - - + +
159A THR 4.1 7.9 - - - +
166A TYR* 3.7 28.3 - - + -
313A ARG* 3.0 38.3 + - + +
314A MET* 3.7 16.2 - - - +
315A ASP 3.3 0.2 - - - -
316A GLU* 1.3 75.7 - - + +
318A ASP* 1.3 63.5 + - - +
320A ARG* 3.4 4.8 + - - +
321A PHE* 3.0 23.4 + - - +
328A LEU* 3.9 20.2 - - + +
331A TYR* 4.1 21.5 - - + +
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Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A THR* 4.6 6.1 - - - -
161A ARG* 2.5 39.6 + - - -
166A TYR* 2.6 36.9 + - - +
314A MET* 3.1 12.5 + - - +
315A ASP* 3.3 9.7 - - - +
317A ILE* 1.3 79.4 - - - +
319A ARG* 1.3 57.8 + - - +
321A PHE* 3.3 3.6 + - - +
322A ALA* 2.9 30.0 + - - +
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ASP 2.8 19.3 + - - +
316A GLU* 2.5 42.1 + - - +
318A ASP* 1.3 74.2 - - - +
320A ARG* 1.3 71.1 + - - +
322A ALA* 3.2 6.2 + - - +
323A GLU* 2.7 72.8 + - - +
324A ASP* 4.8 9.3 + - - +
327A ALA* 5.5 2.0 - - - +
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Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ARG* 5.1 6.7 - - - +
316A GLU* 2.9 55.2 + - - +
317A ILE* 3.8 4.9 - - - +
318A ASP 3.3 0.2 - - - -
319A ARG* 1.3 86.1 - - - +
321A PHE* 1.3 62.9 + - - +
324A ASP* 2.6 51.1 + - + +
325A LYS 4.2 0.2 - - - -
327A ALA* 3.2 27.2 + - + +
328A LEU* 3.9 24.9 - - + +
331A TYR* 3.5 25.1 - - - +
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Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A TYR* 3.4 48.0 - + + -
180A MET* 3.9 7.2 - - - -
181A LEU* 3.5 47.6 - - + -
182A GLY 4.4 2.5 - - - -
185A ASN* 3.3 0.7 + - - -
201A ARG* 5.3 1.1 - - - -
317A ILE 3.0 17.2 + - - +
318A ASP 3.8 3.8 - - - +
320A ARG* 1.3 76.2 - - - +
322A ALA* 1.3 66.5 + - - +
325A LYS* 3.2 56.9 - - - +
328A LEU* 3.8 19.9 - - + +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.1 10.1 + - - -
318A ASP 2.9 17.2 + - - +
319A ARG* 3.5 7.4 - - - +
321A PHE* 1.3 84.5 - - + +
323A GLU* 1.3 62.6 + - + +
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Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.0 22.5 + - - +
186A GLY* 3.7 9.9 + - - -
319A ARG* 2.7 53.2 + - - +
322A ALA* 1.3 78.3 - - + +
324A ASP* 1.3 59.4 + - + +
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Residues in contact with ASP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.6 0.9 - - - -
186A GLY* 4.0 9.2 - - - -
187A ASP 4.4 2.1 + - - +
319A ARG* 4.8 9.6 + - - +
320A ARG* 2.6 23.4 + - - +
323A GLU* 1.3 78.0 - - + +
325A LYS* 1.3 65.0 + - - +
326A PRO* 3.5 13.2 - - - +
327A ALA* 3.0 39.7 + - + +
328A LEU 3.1 8.8 + - - -
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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