Contacts of the helix formed by residues 307 - 323 (chain P) in PDB entry 1ZD2
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 CYS 307 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304P GLU* 3.1 11.2 + - - +
305P GLU 3.6 0.2 - - - -
306P TYR* 1.3 82.6 - - - +
308P MET* 1.3 67.2 + - - +
309P GLU* 3.3 11.1 + - - +
310P VAL* 3.2 40.1 + - - -
311P LEU* 3.0 19.2 + - - +
467P ASN* 3.2 22.5 - - + +
470P ARG* 3.8 22.9 - - + +
471P ASN* 3.4 12.1 - - - +
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Residues in contact with MET 308 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306P TYR 3.7 0.6 + - - -
307P CYS* 1.3 71.2 - - - +
309P GLU* 1.3 62.4 + - - +
311P LEU* 3.3 26.2 - - + -
312P CYS* 2.9 26.4 + - - +
334P TRP* 4.1 25.4 - - - -
337P MET* 4.4 3.8 - - + -
338P LEU* 3.0 48.9 - - + -
341P TYR* 4.2 20.4 - - + -
464P TRP* 3.8 7.4 - - + -
471P ASN* 2.5 33.2 + - + +
474P TRP* 4.0 19.7 - - + -
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Residues in contact with GLU 309 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307P CYS* 3.3 10.4 - - - -
308P MET* 1.3 77.5 - - - +
310P VAL* 1.3 67.8 + - + +
312P CYS* 2.9 4.2 + - - +
313P LYS* 2.7 54.8 + - + +
471P ASN* 4.3 0.8 + - - +
474P TRP* 3.4 56.2 + - + +
477P LYS* 5.1 5.4 + - - -
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Residues in contact with VAL 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243P LYS* 3.3 29.8 - - - +
292P LYS* 3.9 1.1 - - - +
304P GLU* 3.8 10.5 - - + +
305P GLU* 3.8 20.9 - - - +
307P CYS* 3.2 27.2 + - - +
309P GLU* 1.3 78.0 - - + +
311P LEU* 1.3 64.8 + - - +
313P LYS* 3.1 12.3 + - + +
314P GLU* 3.0 31.8 + - - +
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Residues in contact with LEU 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292P LYS* 3.7 39.3 - - + -
305P GLU 4.1 4.7 - - - +
306P TYR* 3.2 29.6 - - + +
307P CYS 3.0 11.6 + - - +
308P MET* 3.3 31.4 - - + -
310P VAL* 1.3 80.0 - - - +
312P CYS* 1.3 62.8 + - - +
314P GLU* 3.5 8.1 + - - +
315P MET* 3.3 24.8 + - - +
338P LEU* 4.2 4.7 - - + -
464P TRP* 3.5 35.4 - - + -
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Residues in contact with CYS 312 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308P MET* 2.9 19.8 + - - +
309P GLU 2.9 3.8 + - - +
311P LEU* 1.3 75.2 - - - +
313P LYS* 1.3 66.7 + - - +
315P MET* 2.9 14.6 + - - +
316P VAL* 3.1 16.0 + - - +
338P LEU* 3.4 29.6 - - - -
341P TYR* 4.2 5.4 - - - -
342P MET* 3.5 34.1 - - - +
346P TYR* 4.3 7.9 - - + -
474P TRP* 4.1 21.1 - - + -
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Residues in contact with LYS 313 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309P GLU* 2.7 54.7 + - + +
310P VAL* 3.6 11.0 - - + +
312P CYS* 1.3 74.3 - - - +
314P GLU* 1.3 58.0 + - + +
316P VAL* 3.1 9.6 + - - +
317P THR* 2.9 32.4 + - - +
346P TYR* 3.5 23.8 + - - +
474P TRP* 5.1 1.0 - - + +
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Residues in contact with GLU 314 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242P VAL* 3.4 22.0 - - + +
243P LYS* 2.9 41.2 + - + +
246P VAL* 3.8 12.8 - - - +
248P LEU* 4.0 6.8 - - + +
292P LYS* 2.7 51.1 + - - +
310P VAL* 3.0 15.0 + - - +
311P LEU* 3.7 14.6 - - - +
313P LYS* 1.3 77.8 - - + +
315P MET* 1.3 58.9 + - + +
317P THR* 3.7 6.5 - - - -
318P PHE* 2.9 22.3 + - - +
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Residues in contact with MET 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248P LEU* 4.1 11.2 - - - -
260P CYS* 3.8 22.9 - - - -
262P CYS* 4.2 9.2 - - - -
289P MET* 3.4 38.4 - - + -
291P MET* 4.4 11.4 - - + -
311P LEU 3.3 13.2 + - - +
312P CYS 2.9 9.7 + - - +
314P GLU* 1.3 75.5 - - - +
316P VAL* 1.3 65.7 + - - +
317P THR 3.2 0.2 - - - -
318P PHE* 3.3 10.1 + - + +
319P LEU* 3.1 26.3 + - - +
329P PHE* 4.1 10.9 - - + -
338P LEU* 4.4 17.9 - - + -
342P MET* 3.9 18.4 - - + -
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Residues in contact with VAL 316 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312P CYS 3.1 12.7 + - - +
313P LYS* 3.1 9.8 + - - +
315P MET* 1.3 74.9 - - - +
317P THR* 1.3 58.7 + - - +
319P LEU* 3.3 11.3 + - - +
320P ASP* 2.9 36.9 + - - +
342P MET* 4.2 7.0 - - + -
346P TYR* 3.5 51.4 - - + -
349P ARG* 4.1 20.6 - - + +
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Residues in contact with THR 317 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242P VAL* 3.4 35.4 + - - +
243P LYS* 6.0 0.9 - - - +
313P LYS* 2.9 15.4 + - - +
314P GLU* 3.5 12.4 - - - -
316P VAL* 1.3 76.3 - - - +
318P PHE* 1.3 64.9 + - - +
320P ASP* 3.8 13.4 + - + +
321P LYS* 2.8 46.5 + - + +
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Residues in contact with PHE 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P VAL* 3.5 37.7 - - + -
242P VAL* 4.0 6.7 - - - -
248P LEU* 4.1 15.5 - - + -
250P PHE* 3.6 25.6 - + - -
260P CYS* 4.6 5.8 - - - -
287P LEU* 4.0 12.3 - - + -
289P MET* 3.4 42.6 - - + -
314P GLU 2.9 16.2 + - - +
315P MET* 3.3 20.0 - - + +
317P THR* 1.3 77.0 - - - +
319P LEU* 1.3 72.6 + - + +
321P LYS* 3.5 2.8 + - - +
322P LEU* 3.2 43.2 + - + +
329P PHE* 6.3 0.2 - + - -
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Residues in contact with LEU 319 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260P CYS* 5.8 2.0 - - + -
287P LEU* 5.9 0.7 - - + -
315P MET 3.1 13.3 + - - +
316P VAL* 3.4 10.8 - - - +
318P PHE* 1.3 87.3 - - + +
320P ASP* 1.3 66.3 + - - +
322P LEU* 2.9 15.1 + - - +
323P GLY 3.0 9.9 + - - -
324P LEU* 3.2 37.8 + - + +
326P GLN 3.8 8.5 - - - +
327P ALA* 3.6 24.0 - - + -
329P PHE* 3.6 29.6 - - + -
342P MET* 5.2 0.4 - - + -
349P ARG* 3.9 32.5 - - + +
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Residues in contact with ASP 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316P VAL* 2.9 28.3 + - - +
317P THR* 3.0 19.2 + - + +
319P LEU* 1.3 77.0 - - - +
321P LYS* 1.3 63.9 + - + +
323P GLY* 3.2 12.0 + - - -
324P LEU 5.0 0.7 - - - +
349P ARG* 2.4 32.9 + - - +
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Residues in contact with LYS 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P VAL* 3.4 30.5 - - + -
241P THR* 3.2 21.0 + - - +
242P VAL* 4.4 4.8 + - - +
317P THR* 2.8 40.3 + - + +
320P ASP* 1.3 73.4 - - + +
322P LEU* 1.3 60.9 + - - +
323P GLY 3.2 0.9 + - - -
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Residues in contact with LEU 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P VAL* 4.1 9.9 - - + -
250P PHE* 3.8 19.1 - - + -
252P GLU* 4.6 1.3 - - - +
285P ARG* 3.7 26.4 + - - +
287P LEU* 4.0 8.1 - - + -
318P PHE* 3.2 58.9 + - + +
319P LEU 2.9 6.2 + - - +
321P LYS* 1.3 76.6 - - - +
323P GLY* 1.3 61.5 + - - +
324P LEU* 3.4 17.0 + - + +
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Residues in contact with GLY 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319P LEU 3.0 3.4 + - - -
320P ASP* 3.2 11.4 + - - -
321P LYS 3.2 2.2 + - - -
322P LEU* 1.3 78.3 - - - +
324P LEU* 1.3 61.3 + - - +
325P SER 3.9 2.1 + - - -
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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
------------------------------------------------------------
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