Contacts of the helix formed by residues 301 - 312 (chain A) in PDB entry 5ZRV
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 PRO 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A VAL* 6.2 4.5 - - - -
298A TYR* 4.2 4.6 - - - -
299A PRO 3.9 0.2 - - - -
300A ALA* 1.3 74.2 - - - +
302A LEU* 1.3 57.8 + - - +
304A ILE* 3.0 17.7 + - - +
305A ILE* 3.6 5.2 + - - -
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Residues in contact with LEU 302 (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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298A TYR 4.9 5.1 + - - -
299A PRO 5.0 0.6 + - - -
300A ALA 3.4 0.4 - - - -
301A PRO* 1.3 75.7 - - - +
303A LYS* 1.3 55.8 + - - +
304A ILE 3.1 0.2 - - - -
305A ILE* 2.9 19.2 + - - +
306A ASP* 3.2 10.2 + - - -
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Residues in contact with LYS 303 (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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299A PRO 4.4 6.1 + - - -
300A ALA 3.1 14.9 + - - -
302A LEU* 1.3 75.2 - - - +
304A ILE* 1.3 55.0 + - - -
306A ASP* 4.6 4.0 - - - +
307A VAL 4.9 3.7 + - - -
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Residues in contact with ILE 304 (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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300A ALA 3.9 1.0 + - - -
301A PRO* 3.0 12.5 + - - +
303A LYS* 1.3 76.1 - - - +
305A ILE* 1.3 64.0 + - - +
306A ASP 3.4 0.9 - - - -
307A VAL* 3.5 6.4 + - - +
308A VAL* 3.5 14.2 + - - -
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Residues in contact with ILE 305 (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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301A PRO 3.6 4.2 + - - -
302A LEU* 2.9 12.2 + - - +
304A ILE* 1.3 79.0 - - - +
306A ASP* 1.3 51.0 + - - +
308A VAL* 2.9 4.8 + - - +
309A LYS* 2.5 35.2 + - - -
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Residues in contact with ASP 306 (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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302A LEU 3.2 9.8 + - - -
303A LYS* 4.6 2.4 - - - +
304A ILE 3.4 0.4 - - - +
305A ILE* 1.3 72.0 - - - +
307A VAL* 1.3 59.8 + - - +
309A LYS* 3.8 4.2 - - - +
310A THR* 3.0 23.4 + - - -
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Residues in contact with VAL 307 (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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303A LYS 4.9 2.6 + - - -
304A ILE* 3.5 10.7 + - - +
305A ILE 3.1 1.0 - - - -
306A ASP* 1.3 75.2 - - - +
308A VAL* 1.3 50.8 + - - +
310A THR 2.9 3.5 + - - -
311A GLY* 2.5 36.3 + - - -
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Residues in contact with VAL 308 (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 THR 5.5 6.5 - - - -
304A ILE 3.5 8.2 + - - -
305A ILE* 2.9 8.2 + - - +
307A VAL* 1.3 72.5 - - - +
309A LYS* 1.3 60.9 + - - +
311A GLY* 4.0 4.3 - - - +
312A ILE* 3.7 13.5 + - - -
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Residues in contact with LYS 309 (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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305A ILE 2.5 21.1 + - - -
306A ASP* 3.9 3.8 - - - +
308A VAL* 1.3 75.7 - - - +
310A THR* 1.3 56.6 + - - +
312A ILE* 3.4 13.5 + - - +
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Residues in contact with THR 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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306A ASP 3.0 12.7 + - - -
307A VAL 2.9 5.5 + - - -
309A LYS* 1.3 73.4 - - - +
311A GLY* 1.3 62.4 + - - +
312A ILE 3.0 13.9 - - - +
314A GLN* 3.8 13.5 + - - -
315A GLY 5.1 2.3 - - - +
319A GLY* 5.8 1.8 - - - -
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Residues in contact with GLY 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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186A GLN* 6.4 1.8 - - - -
307A VAL 2.5 21.6 + - - -
308A VAL* 4.0 2.9 - - - -
310A THR* 1.3 73.6 - - - +
312A ILE* 1.3 58.9 + - - +
313A GLU 3.7 1.4 + - - -
314A GLN 3.8 11.4 - - - +
315A GLY 5.5 1.3 - - - -
316A SER* 4.6 12.2 - - - -
319A GLY* 5.7 5.6 - - - -
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Residues in contact with ILE 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 VAL* 3.7 14.5 + - - +
309A LYS 3.4 10.0 - - - +
310A THR* 3.0 13.6 - - - +
311A GLY* 1.3 74.9 - - - +
313A GLU* 1.3 52.7 + - - +
314A GLN 2.9 11.8 + - - -
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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