Contacts of the helix formed by residues 297 - 302 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ARG 5.8 1.3 - - - +
310A VAL* 3.4 32.1 - - + +
313A TRP* 3.7 29.1 - - + +
314A SER* 5.4 1.3 - - - +
371A ARG* 4.3 0.2 - - - +
295D TYR 4.1 4.0 - - - +
296D LEU* 1.4 91.7 - - + +
298D PRO* 1.3 77.3 - - + +
299D GLU* 3.5 20.0 - - - +
300D MET* 3.3 18.8 + - + -
301D ILE* 3.0 21.9 + - - +
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Residues in contact with PRO 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A TRP* 3.8 26.5 - - + -
341A ILE* 3.8 23.9 - - + +
342A SER* 4.7 4.0 - - - -
366A HIS* 4.1 33.2 - - + +
371A ARG* 4.2 0.9 - - - +
297D PRO* 1.3 89.6 - - + +
299D GLU* 1.3 60.6 + - - +
301D ILE* 3.3 11.8 - - + +
302D GLU* 2.7 50.9 + - - +
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Residues in contact with GLU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A GLU* 6.6 0.4 - - + -
303A GLY* 6.4 2.2 - - - -
306A HIS 5.0 1.4 - - - +
310A VAL* 3.6 25.0 + - + +
366A HIS 4.2 2.9 - - - +
368A PRO* 3.8 23.1 - - + +
371A ARG* 2.6 47.6 + - - -
297D PRO* 3.5 11.0 - - - +
298D PRO* 1.3 80.4 - - - +
300D MET* 1.3 66.6 + - + +
302D GLU* 2.7 20.8 - - - +
303D GLY* 4.8 1.0 - - - -
304D ARG* 4.6 1.2 + - - +
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Residues in contact with MET 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ARG* 3.9 43.5 - - + +
303A GLY* 5.6 9.4 - - - -
307A ASP* 5.4 4.5 - - + -
310A VAL* 4.1 22.0 - - + -
296D LEU* 4.8 12.3 - - + -
297D PRO* 3.3 32.0 + - + -
298D PRO 3.3 0.2 - - - -
299D GLU* 1.3 87.6 - - + +
301D ILE* 1.3 70.1 + - - +
302D GLU 3.4 0.2 - - - +
304D ARG* 3.1 46.2 - - - +
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Residues in contact with ILE 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A TYR* 3.0 43.9 - - + +
341A ILE* 3.3 39.7 - - + -
342A SER* 6.0 2.2 - - - -
293D LEU* 4.9 6.3 - - + -
296D LEU* 3.3 45.2 - - + +
297D PRO 3.0 12.4 + - - +
298D PRO* 3.3 7.0 - - + +
300D MET* 1.3 75.8 - - - +
302D GLU* 1.3 58.2 + - + +
304D ARG 2.5 24.6 - - - +
305D MET* 4.4 4.9 - - - +
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Residues in contact with GLU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TYR* 3.0 34.3 + - + +
342A SER* 4.1 16.9 + - - -
366A HIS* 4.9 5.0 + - - -
298D PRO* 2.7 34.0 + - - +
299D GLU* 2.7 24.1 - - - +
300D MET 3.4 0.5 - - - +
301D ILE* 1.3 73.8 - - + +
303D GLY* 1.3 53.3 + - - +
304D ARG 2.6 20.8 + - - -
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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