Contacts of the helix formed by residues 309 - 324 (chain B) in PDB entry 4MZ7
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 ASP 309 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B LEU* 6.4 0.9 - - - -
299B GLU 4.4 0.7 - - - -
300B ILE 3.2 15.3 - - - +
301B VAL 3.5 14.1 - - - +
302B SER* 3.5 3.5 + - - -
303B ASN* 3.0 30.5 + - + +
307B GLY* 3.1 8.5 + - - +
308B ILE* 1.3 76.0 - - - +
310B VAL* 1.3 62.1 - - - +
311B ASP* 3.3 4.8 + - - +
312B LYS* 3.3 17.6 + - - +
313B TRP* 3.3 25.6 - - - +
804B DGT 2.8 30.4 + - - -
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 3.8 29.9 - - + +
174B LEU* 3.7 34.0 - - + +
175B ALA* 3.9 11.7 - - + +
178B LEU* 4.2 7.2 - - + -
300B ILE* 2.9 31.6 + - + +
301B VAL* 4.2 5.4 - - - -
309B ASP* 1.3 70.3 - - - +
311B ASP* 1.3 66.2 + - - +
312B LYS 3.3 0.2 - - - -
313B TRP* 3.6 33.1 - - + +
314B ASP* 3.0 22.0 + - - +
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Residues in contact with ASP 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B HIS* 3.0 12.5 + - - -
171B VAL* 3.9 10.8 - - + -
206B HIS* 3.1 14.5 + - + +
207B ASP* 5.0 0.3 - - - +
301B VAL 3.6 14.4 + - - +
302B SER* 6.1 0.3 - - - -
309B ASP* 3.2 11.4 - - - +
310B VAL* 1.3 81.4 - - - +
312B LYS* 1.3 62.9 + - - +
314B ASP 3.3 0.3 + - - -
315B TYR* 3.0 24.6 + - - -
803B ZN 2.1 36.7 - - - -
804B DGT 2.9 28.0 + - - +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B GLY* 2.7 37.1 + - - +
309B ASP* 3.3 9.9 + - - +
311B ASP* 1.3 79.0 - - - +
313B TRP* 1.3 64.1 + - + +
315B TYR* 3.6 15.0 - - + +
316B PHE* 2.8 48.5 + - + -
362B MET* 3.8 17.0 - - + -
363B PHE* 4.3 11.0 - - - -
366B ARG* 3.7 21.0 - - - +
508B GLY* 6.2 2.3 - - - -
804B DGT 2.5 60.8 + - - +
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Residues in contact with TRP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B HIS* 5.5 0.2 - - - -
174B LEU* 3.9 10.5 - - + +
178B LEU* 4.1 15.3 - - + -
308B ILE* 3.9 15.3 - - + +
309B ASP* 3.3 20.2 + - - -
310B VAL* 3.3 32.0 + - + +
311B ASP 3.2 1.0 - - - -
312B LYS* 1.3 83.9 - - + +
314B ASP* 1.3 63.9 + - - +
316B PHE* 3.7 6.2 + + - +
317B ALA* 3.4 19.6 + - - +
327B ASN* 5.1 0.7 + - - -
329B PHE* 3.4 30.1 - + - -
331B TYR* 3.6 36.3 - + + -
334B PHE* 3.4 43.5 - + + -
335B ILE* 3.7 24.9 - - + -
362B MET* 3.8 13.2 - - - -
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Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ILE* 5.1 0.2 - - - +
123B HIS* 2.7 29.6 + - - -
167B HIS* 2.8 32.6 + - - +
170B GLY* 3.3 3.9 - - - -
171B VAL* 3.8 22.2 - - + +
174B LEU* 3.7 11.1 - - + +
310B VAL 3.0 10.5 + - - +
311B ASP 3.8 0.2 - - - +
313B TRP* 1.3 77.5 - - - +
315B TYR* 1.3 56.6 + - - +
317B ALA* 3.3 2.5 + - - +
318B ARG* 2.8 58.8 + - - +
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Residues in contact with TYR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B GLN* 4.0 3.6 - - - +
167B HIS* 3.9 13.5 - + + -
311B ASP* 3.0 28.0 + - - +
312B LYS* 3.6 10.4 - - + +
314B ASP* 1.3 77.5 - - - +
316B PHE* 1.3 86.2 + + - +
318B ARG* 4.4 2.0 - - - +
319B ASP* 2.8 41.1 + - - +
366B ARG* 3.7 15.8 + - + +
370B HIS* 4.7 0.3 + - - -
374B TYR* 3.4 28.9 - + - -
804B DGT 2.6 91.6 + - - +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B LYS* 2.8 40.4 + - + +
313B TRP* 3.9 4.0 - - - +
315B TYR* 1.3 106.4 - + - +
317B ALA* 1.3 63.4 + - - +
319B ASP* 4.5 0.3 - - - +
320B CYS* 3.1 28.4 + - - +
327B ASN* 3.8 14.8 - - - +
329B PHE* 4.0 24.7 - + + -
362B MET* 3.5 46.4 - - + -
365B THR* 4.1 9.9 - - + -
366B ARG* 3.7 23.8 - - + -
369B LEU* 3.8 16.2 - - + -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ILE* 3.6 24.9 - - + +
123B HIS* 5.2 2.7 - - + -
313B TRP 3.4 13.1 + - - +
314B ASP* 3.3 3.4 + - - +
316B PHE* 1.3 79.2 - - - +
318B ARG* 1.3 59.4 + - - +
320B CYS* 3.8 1.4 - - - +
321B HIS* 3.0 28.6 + - - +
327B ASN* 3.6 18.1 - - - +
331B TYR* 5.7 7.2 - - + -
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY* 5.7 0.6 - - - -
120B ASP* 2.8 41.4 + - - -
121B PRO* 4.7 5.5 - - - +
122B ILE* 3.5 24.2 - - + +
123B HIS* 3.5 7.5 - - - -
149B GLN* 5.9 0.2 - - - -
162B HIS* 3.9 20.0 - - + -
166B GLU* 3.5 31.7 + - - +
167B HIS* 3.5 22.8 - - - +
170B GLY* 3.8 2.0 - - - -
314B ASP* 2.8 57.7 + - - +
315B TYR* 4.4 2.2 - - - +
317B ALA* 1.3 71.7 - - - +
319B ASP* 1.3 68.4 + - - +
321B HIS* 3.3 1.7 + - - +
322B HIS* 3.0 39.9 + - + +
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Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B GLN* 3.7 6.1 + - - +
150B LEU* 3.9 7.4 - - + -
162B HIS* 2.8 30.0 + - - +
315B TYR* 2.8 28.3 + - - +
316B PHE 4.5 0.7 - - - +
318B ARG* 1.3 71.0 - - - +
320B CYS* 1.3 53.5 + - - +
322B HIS* 3.1 1.6 + - - +
323B LEU* 2.7 52.9 + - + +
369B LEU* 5.5 0.4 - - + -
374B TYR* 2.6 30.3 + - + +
804B DGT 2.6 28.2 + - - -
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Residues in contact with CYS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B PHE 3.1 24.5 + - - +
317B ALA 3.8 3.4 - - - +
319B ASP* 1.3 78.1 - - - +
321B HIS* 1.3 62.7 + - - +
323B LEU* 4.5 3.6 - - - -
324B GLY* 3.0 18.2 + - - -
325B ILE* 3.0 31.8 + - - +
326B GLN 3.9 3.4 - - - -
327B ASN* 3.7 30.5 - - + +
365B THR* 5.9 0.7 - - - -
369B LEU* 3.7 32.8 - - - -
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Residues in contact with HIS 321 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A PRO* 3.5 6.6 - - - +
321A HIS* 2.8 87.7 + + - -
322A HIS* 5.5 0.4 - - - -
121B PRO* 3.8 17.7 + - + +
122B ILE* 3.5 23.4 - - + +
317B ALA 3.0 19.0 + - - +
318B ARG 3.4 6.1 - - - +
320B CYS* 1.3 76.1 - - - +
322B HIS* 1.3 77.2 + + - +
324B GLY* 4.1 0.7 + - - -
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Residues in contact with HIS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO* 3.4 8.5 - - - +
159A GLY* 4.2 6.3 + - - -
161A SER* 4.1 4.2 + - - -
321A HIS* 4.8 0.9 - - - -
322A HIS* 3.7 29.8 - + - -
121B PRO* 5.0 8.9 - - + +
122B ILE* 5.1 0.2 - - + -
159B GLY* 3.1 48.8 - - - +
161B SER* 4.2 3.1 - - - -
162B HIS* 3.5 50.9 - + + +
166B GLU* 5.9 1.1 - - + -
318B ARG* 3.0 34.1 + - + +
319B ASP 3.1 1.4 + - - -
320B CYS 3.1 0.4 - - - -
321B HIS* 1.3 94.9 - + - +
323B LEU* 1.3 65.0 + - - +
324B GLY 3.3 0.4 - - - -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN* 3.6 15.8 + - - +
121A PRO* 4.6 2.3 - - - +
150B LEU* 3.7 25.6 - - + -
153B GLY* 6.1 0.7 - - - -
157B PHE* 3.4 59.4 - - + +
159B GLY 5.6 0.3 + - - -
160B ALA* 4.1 3.8 - - + +
319B ASP* 2.7 43.9 + - + +
320B CYS* 4.1 3.8 - - - +
322B HIS* 1.3 74.1 - - - +
324B GLY* 1.3 60.4 + - - +
325B ILE* 4.1 17.9 - - + +
369B LEU* 5.1 4.9 - - + -
373B ALA* 3.7 24.0 - - + -
374B TYR* 4.5 4.0 - - + -
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Residues in contact with GLY 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN* 3.3 20.8 + - - +
120A ASP 4.8 0.4 - - - -
121A PRO* 3.9 23.9 - - - +
125A HIS* 5.6 1.4 - - - -
320B CYS 3.0 7.6 + - - -
321B HIS 4.7 0.7 - - - -
322B HIS 3.3 2.6 - - - -
323B LEU* 1.3 79.4 - - - +
325B ILE* 1.3 60.5 + - - +
326B GLN* 6.1 0.2 - - - -
805B DTP 5.1 0.5 - - - -
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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
------------------------------------------------------------
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