Contacts of the helix formed by residues 314 - 327 (chain A) in PDB entry 3RCY
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 GLY 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TRP* 3.4 21.2 - - - -
39A GLU* 2.7 23.9 + - - +
311A LEU* 3.4 8.1 - - - +
313A ALA* 1.3 75.4 - - - +
315A PRO* 1.3 75.1 - - - +
316A VAL 3.2 3.5 + - - -
317A GLU* 3.6 0.5 + - - +
318A TRP 3.3 14.9 + - - -
342A HIS* 4.0 3.4 - - - -
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Residues in contact with PRO 315 (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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23A TRP* 3.6 17.9 - - + -
25A LEU* 5.9 0.2 - - + -
39A GLU* 4.7 0.2 - - - +
314A GLY* 1.3 82.3 - - - +
316A VAL* 1.3 60.2 + - + +
318A TRP* 3.6 15.7 - - + +
319A ALA* 2.9 26.3 + - - +
342A HIS* 3.4 39.5 - - + +
345A LEU* 3.8 19.5 - - + -
346A ILE* 3.8 36.7 - - + +
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Residues in contact with VAL 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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25A LEU* 4.1 17.9 - - + -
37A TRP* 3.9 10.5 - - + +
38A GLY* 3.4 42.2 - - - +
39A GLU* 3.4 9.6 + - + +
99A ILE* 4.8 1.2 - - + +
314A GLY 3.2 1.4 - - - -
315A PRO* 1.3 78.5 - - + +
317A GLU* 1.3 65.9 + - - +
319A ALA* 3.1 12.5 + - - +
320A ALA* 3.2 11.6 + - - +
345A LEU* 5.4 1.8 - - + -
346A ILE* 4.4 4.9 - - + -
365A LEU* 4.6 3.5 - - + +
367A ILE* 4.1 13.0 - - + -
369A VAL* 4.0 30.3 - - + -
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Residues in contact with GLU 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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39A GLU* 2.8 34.9 + - + +
41A TYR* 3.8 8.9 - - - +
99A ILE* 4.8 5.4 - - + -
283A ALA* 3.6 12.1 - - - +
284A LEU* 3.6 11.3 + - + +
285A GLY* 2.9 39.7 + - - +
310A HIS* 3.8 11.6 + - - +
311A LEU* 3.5 19.9 - - - +
312A TYR 4.7 0.5 + - - -
313A ALA* 3.7 13.8 - - - +
314A GLY 4.0 2.7 - - - +
316A VAL* 1.3 72.6 - - - +
318A TRP* 1.3 62.7 + - - +
320A ALA* 3.2 8.4 + - - +
321A ASN* 3.0 31.3 + - - +
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Residues in contact with TRP 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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311A LEU* 3.7 28.0 - - + +
314A GLY 3.3 7.4 + - - +
315A PRO* 3.6 19.1 - - + +
316A VAL 3.1 0.4 - - - -
317A GLU* 1.3 78.6 - - - +
319A ALA* 1.3 62.2 + - - +
321A ASN* 3.2 15.7 + - + +
322A VAL* 3.0 29.0 + - + +
334A CYS* 4.7 2.0 - - + +
335A GLU 3.3 18.1 + - - -
336A SER* 3.2 25.4 + - - -
337A ILE 5.6 0.7 - - - -
342A HIS* 6.0 0.4 - + + -
346A ILE* 4.7 6.7 - - + -
350A ILE* 3.3 50.7 - - + -
351A ARG* 4.0 15.3 - - - -
352A VAL* 3.8 8.1 - - + -
357A ILE* 3.5 29.3 - - + +
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Residues in contact with ALA 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 PRO 2.9 15.0 + - - +
316A VAL 3.1 9.4 + - - +
318A TRP* 1.3 73.3 - - - +
320A ALA* 1.3 66.5 + - - +
322A VAL* 3.2 3.8 + - - +
323A HIS* 3.1 31.0 + - - -
350A ILE* 3.7 29.2 - - + -
365A LEU* 4.1 14.1 - - + +
367A ILE* 3.8 18.2 - - + -
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Residues in contact with ALA 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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99A ILE* 3.8 43.1 - - + -
284A LEU* 3.9 11.6 - - + +
290A ILE* 4.0 11.5 - - + +
316A VAL 3.2 5.0 + - - +
317A GLU 3.2 9.5 + - - +
319A ALA* 1.3 79.3 - - - +
321A ASN* 1.3 63.0 + - - +
322A VAL 3.3 0.2 + - - -
323A HIS* 3.4 1.7 + - - +
324A PHE* 3.0 25.3 + - - +
365A LEU* 4.0 11.3 - - - +
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Residues in contact with ASN 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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284A LEU* 3.6 30.0 + - - +
309A PRO* 3.6 22.7 + - + +
310A HIS 3.0 29.7 + - - +
311A LEU* 4.0 9.7 - - - +
317A GLU* 3.0 22.6 + - - +
318A TRP* 3.2 24.2 - - + +
320A ALA* 1.3 76.1 - - - +
322A VAL* 1.3 56.9 + - - +
324A PHE* 3.6 4.0 - - - +
325A ALA* 2.8 31.4 + - - +
334A CYS* 4.0 6.9 - - - +
335A GLU 4.9 0.4 + - - -
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Residues in contact with VAL 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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125A ILE* 3.4 14.0 - - + +
318A TRP* 3.0 39.0 + - + +
319A ALA* 3.2 9.8 + - - +
321A ASN* 1.3 74.2 - - + +
323A HIS* 1.3 60.5 + - + +
325A ALA* 3.3 4.3 + - - -
326A ALA* 2.8 28.9 + - - +
334A CYS* 4.8 2.5 - - - -
350A ILE* 4.4 8.1 - - + -
357A ILE* 3.9 39.0 - - + -
359A PRO* 4.3 4.0 - - + -
360A PRO* 4.0 24.2 - - + -
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Residues in contact with HIS 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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112A PRO* 3.9 5.4 - - + -
113A VAL* 3.5 26.4 + - + -
114A TRP* 3.2 60.7 + + - +
117A LEU* 3.9 2.8 - - - +
290A ILE* 5.5 0.7 - - + -
319A ALA* 3.1 26.7 + - - +
320A ALA* 3.9 2.9 - - - +
322A VAL* 1.3 73.3 - - + +
324A PHE* 1.3 67.5 + - - +
326A ALA* 3.4 5.9 + - - -
327A SER* 3.5 6.4 + - - -
350A ILE* 5.0 0.4 - - + -
360A PRO* 3.4 21.2 - - + +
362A ALA 5.2 0.2 - - - -
364A GLY 3.4 18.4 - - - -
365A LEU* 2.8 39.7 + - + -
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Residues in contact with PHE 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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117A LEU* 4.3 6.7 - - - +
282A PRO* 5.2 0.7 - - + -
284A LEU* 3.9 25.4 - - + -
290A ILE* 4.2 12.5 - - + +
293A MET* 3.3 39.9 - - + -
294A LYS* 3.6 22.9 - - + -
297A ALA* 3.9 17.0 - - + -
307A MET* 4.1 17.3 - - + -
309A PRO* 3.8 27.8 - - + -
320A ALA 3.0 17.5 + - - +
321A ASN 3.6 1.6 - - - +
323A HIS* 1.3 75.6 - - - +
325A ALA* 1.3 63.6 + - - +
327A SER* 2.8 23.8 + - - -
328A ILE* 3.6 23.7 + - + +
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Residues in contact with ALA 325 (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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122A ASN* 2.8 29.6 + - - -
125A ILE* 4.0 10.1 - - + -
309A PRO* 4.8 1.3 - - + -
321A ASN 2.8 21.0 + - - +
322A VAL 3.7 3.6 - - - +
324A PHE* 1.3 76.0 - - - +
326A ALA* 1.3 54.4 + - - +
327A SER 3.1 1.0 + - - -
328A ILE* 3.5 15.8 + - - +
331A ILE* 3.6 19.6 - - + +
334A CYS* 3.5 24.0 - - - -
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Residues in contact with ALA 326 (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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114A TRP* 3.7 18.4 - - + -
119A GLY 4.4 1.1 - - - -
120A LYS* 3.7 3.4 - - + -
121A MET* 2.8 31.4 + - - -
122A ASN* 3.1 14.1 + - - +
125A ILE* 3.7 6.9 - - - +
322A VAL 2.8 20.8 + - - +
323A HIS 3.7 7.0 - - - +
324A PHE 3.3 0.2 - - - -
325A ALA* 1.3 72.6 - - - +
327A SER* 1.3 49.4 + - - +
328A ILE 3.6 0.2 - - - -
359A PRO* 3.7 30.3 - - + -
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Residues in contact with SER 327 (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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114A TRP* 4.0 4.5 - - - -
117A LEU* 3.6 27.0 - - - +
119A GLY 3.3 17.5 - - - -
121A MET* 3.8 4.8 - - - +
294A LYS* 3.0 30.8 + - - +
323A HIS 3.5 7.6 + - - -
324A PHE 2.8 18.1 + - - -
325A ALA 3.1 0.2 - - - -
326A ALA* 1.3 79.5 - - - +
328A ILE* 1.3 57.9 + - - +
71D GLU* 3.5 19.4 - - - +
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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
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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