Contacts of the helix formed by residues 297 - 307 (chain A) in PDB entry 4C3P
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 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A TYR 4.2 1.1 - - - +
296A LEU* 1.3 94.1 - - + +
298A PRO* 1.3 80.9 - - + +
299A GLU* 3.6 19.1 - - - +
300A MET* 2.9 23.5 + - + -
301A ILE* 3.2 10.0 + - - +
255D ARG 6.1 0.4 - - - +
256D ASP* 5.3 1.1 - - - +
310D VAL* 3.4 31.0 - - + +
313D TRP* 3.5 34.8 - - + +
314D SER* 5.3 2.5 - - - +
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Residues in contact with PRO 298 (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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297A PRO* 1.3 85.3 - - + +
299A GLU* 1.3 73.2 + - - +
301A ILE* 2.8 25.4 + - + +
302A GLU* 3.0 23.0 + - + +
313D TRP* 3.8 23.6 - - + -
341D ILE* 3.7 24.3 - - + +
342D SER* 4.6 11.2 - - - -
344D VAL* 4.8 1.1 - - + -
366D HIS* 4.5 32.1 - - + +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO* 3.6 15.3 - - + +
298A PRO* 1.3 78.2 - - - +
300A MET* 1.3 63.2 + - + +
302A GLU* 4.2 4.6 - - - +
303A GLY* 2.9 25.5 + - - -
303D GLY* 4.4 20.7 - - - +
306D HIS 4.9 2.6 - - - +
310D VAL* 4.1 10.8 + - + +
366D HIS 3.7 2.9 - - - +
368D PRO* 3.5 28.2 - - + +
371D ARG* 2.5 47.8 + - - -
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Residues in contact with MET 300 (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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289A LEU* 4.7 0.5 - - - +
296A LEU* 4.1 13.0 - - + -
297A PRO* 2.9 19.7 + - + +
298A PRO 2.9 1.2 + - - -
299A GLU* 1.3 83.3 - - + +
301A ILE* 1.3 65.7 + - - +
303A GLY* 3.9 6.0 - - - -
304A ARG* 3.4 57.7 + - + +
255D ARG* 3.6 42.2 - - - +
256D ASP* 4.8 1.6 - - - +
310D VAL* 3.5 26.7 - - + -
1392D SO4 4.6 8.3 - - - +
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Residues in contact with ILE 301 (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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289A LEU* 4.2 19.6 - - + +
293A LEU* 4.3 9.0 - - + -
296A LEU* 3.3 34.5 - - + +
297A PRO 3.4 7.2 - - - +
298A PRO* 2.8 6.4 + - + +
300A MET* 1.3 79.5 - - - +
302A GLU* 1.3 60.0 + - - +
304A ARG* 3.5 2.4 + - - -
305A MET* 3.1 29.4 + - + +
338D TYR* 3.2 40.2 - - + +
341D ILE* 3.4 40.6 - - + -
342D SER 5.8 0.2 - - - +
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PRO* 3.0 20.0 + - + +
299A GLU* 4.2 3.8 - - - +
301A ILE* 1.3 79.3 - - - +
303A GLY* 1.3 68.0 + - - +
304A ARG 3.2 0.3 + - - -
305A MET* 3.2 11.4 + - - +
306A HIS* 3.3 32.4 + - - +
307A ASP 4.4 0.2 + - - -
368A PRO* 5.9 6.3 - - + +
299D GLU* 6.6 0.2 - - + -
338D TYR* 2.8 37.8 + - - -
342D SER* 4.9 10.0 - - - -
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Residues in contact with GLY 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 GLU 2.9 19.6 + - - -
300A MET* 4.1 7.6 - - - -
301A ILE 3.4 0.2 - - - -
302A GLU* 1.3 79.5 - - - +
304A ARG* 1.3 58.4 + - - +
307A ASP* 3.1 33.0 + - - +
299D GLU* 6.4 2.2 - - - -
300D MET* 5.6 10.3 - - - +
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Residues in contact with ARG 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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282A PRO* 6.1 3.1 - - + -
285A ARG* 3.9 21.3 + - + +
288A THR* 6.4 0.4 - - - -
289A LEU* 3.5 27.4 - - + +
292A THR* 4.8 2.2 - - - +
296A LEU* 3.5 20.6 - - - +
300A MET* 3.4 40.2 + - + +
301A ILE 4.2 0.9 - - - +
302A GLU 3.2 0.6 - - - -
303A GLY* 1.3 74.4 - - - +
305A MET* 1.3 67.0 + - - +
307A ASP* 3.9 17.7 - - - +
255D ARG* 4.5 6.1 - - - +
256D ASP* 3.0 35.0 + - - -
277D TRP* 3.1 51.0 - - + +
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Residues in contact with MET 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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285A ARG* 3.4 44.3 + - - +
286A ARG* 6.4 2.2 - - + -
289A LEU* 3.5 26.9 - - + -
293A LEU* 5.9 2.0 - - + -
301A ILE* 3.1 30.4 + - + +
302A GLU* 3.2 7.5 + - - +
304A ARG* 1.3 79.9 - - - +
306A HIS* 1.3 87.9 + - + +
307A ASP* 3.8 2.2 + - - +
308A GLU* 5.1 3.6 - - - +
338D TYR* 4.6 14.4 - - + +
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Residues in contact with HIS 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 GLU* 3.3 23.8 + - - +
303A GLY 4.0 0.7 - - - -
305A MET* 1.3 100.7 - - + +
307A ASP* 1.3 55.5 + - - +
308A GLU* 3.1 5.2 - - - +
309A LYS* 2.7 43.2 + - + +
310A VAL* 3.7 3.3 + - - +
368A PRO* 3.7 28.7 - - + +
369A SER* 3.8 34.4 + - - -
299D GLU* 5.0 0.7 - - - +
338D TYR* 5.5 1.3 - - - -
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Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ILE* 3.7 29.5 - - + +
255A ARG* 3.9 24.2 + - - +
279A VAL* 5.5 0.5 - - - +
281A ALA* 5.2 4.4 - - - +
282A PRO* 5.3 6.4 - - - +
285A ARG* 5.5 3.3 - - - -
303A GLY 3.1 21.9 + - - +
304A ARG* 3.9 21.1 - - - +
305A MET 4.5 1.0 - - - +
306A HIS* 1.3 72.3 + - - +
308A GLU* 1.3 72.5 + - - +
310A VAL* 2.9 32.7 + - + +
299D GLU* 6.4 0.2 - - - -
300D MET* 5.4 3.1 - - + -
1392D SO4 5.3 1.2 + - - -
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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