Contacts of the helix formed by residues 4357 - 4364 (chain D) in PDB entry 2H7C
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 TRP4357 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2367B PRO* 4.5 14.0 + - + -
2369B SER* 4.8 19.6 - - - +
2370B GLU* 5.1 2.5 - - + -
4100D LEU* 4.9 2.0 - - + -
4355D PHE 3.5 1.6 - - - -
4356D GLY* 1.3 80.6 - - - +
4358D LEU* 1.3 92.8 + - + +
4359D ILE 3.5 1.8 - - - -
4360D PRO* 3.2 9.4 - - - +
4361D MET* 3.0 65.4 + - + +
4457D SER* 3.8 28.9 - - - -
4459D MET* 3.7 30.0 + - + -
4460D LYS* 3.8 27.1 - - + -
4461D PRO* 3.7 24.2 - - + +
4464D VAL* 4.0 13.7 - - + -
4467D ASP* 3.1 16.5 + - - +
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Residues in contact with LEU4358 (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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4D COA 5.6 1.1 - - + +
4097D LEU* 5.0 0.7 - - + -
4100D LEU* 3.5 36.3 - - + -
4101D PHE* 3.4 37.5 - - + -
4357D TRP* 1.3 89.5 - - + +
4359D ILE* 1.3 57.9 + - + +
4361D MET* 3.2 3.7 + - + +
4363D LEU* 2.8 51.7 + - + +
4467D ASP* 2.8 26.1 + - - +
4468D HIS* 3.6 25.6 - - + +
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Residues in contact with ILE4359 (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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4D COA 4.7 22.0 - - + +
4354D GLU 3.4 21.5 - - - +
4355D PHE* 3.4 25.4 - - + -
4357D TRP 4.9 0.2 - - - +
4358D LEU* 1.3 76.5 - - + +
4360D PRO* 1.3 65.2 - - + +
4363D LEU* 3.0 7.7 + - - -
4364D MET* 2.8 47.9 + - + +
4388D LEU* 5.4 0.4 - - + -
4425D MET* 5.5 1.8 - - + -
4426D PHE* 3.9 24.7 - - + -
4467D ASP* 5.0 0.8 + - - -
4468D HIS* 3.7 33.2 - - + +
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Residues in contact with PRO4360 (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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2369B SER* 4.9 6.7 - - - +
4355D PHE* 3.7 42.4 - - + +
4356D GLY 4.4 1.3 - - - +
4357D TRP* 3.2 24.7 - - - +
4359D ILE* 1.3 95.2 - - + +
4361D MET* 1.3 58.9 + - - +
4365D SER* 3.1 3.6 + - - -
4366D TYR* 2.9 56.3 + - + +
4368D LEU* 4.2 11.7 - - + -
4418D LEU* 4.9 2.7 - - + -
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Residues in contact with MET4361 (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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2308B LEU* 3.8 9.2 - - + -
2365B SER 5.3 2.5 - - - +
2367B PRO* 4.1 27.6 - - + -
2369B SER* 6.1 3.5 - - - -
4D COA 3.1 42.8 + - - +
4096D LEU* 4.6 4.0 - - + -
4100D LEU* 3.9 20.0 - - + -
4357D TRP* 3.0 53.0 + - + +
4358D LEU* 3.4 5.6 - - + +
4360D PRO* 1.3 76.6 - - - +
4363D LEU* 1.3 88.1 + - + +
4365D SER* 3.3 11.8 + - - +
4459D MET* 5.6 2.0 - - + -
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Residues in contact with LEU4363 (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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4D COA 2.9 106.4 + - + +
4096D LEU* 3.8 17.9 - - + -
4097D LEU* 4.6 3.1 - - + +
4100D LEU* 4.4 3.1 - - + -
4358D LEU* 2.8 42.8 + - + +
4359D ILE* 3.6 6.1 - - - +
4361D MET* 1.3 100.3 - - + +
4364D MET* 1.3 58.1 + - + +
4365D SER* 3.4 3.3 + - - -
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Residues in contact with MET4364 (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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4D COA 4.9 9.6 - - + -
4304D LEU* 3.5 36.8 - - + +
4305D SER* 3.7 10.5 - - - +
4306D LEU* 3.0 26.8 + - + +
4317D PRO* 4.1 14.1 - - + -
4318D LEU* 5.0 3.8 - - + -
4359D ILE* 2.8 39.1 + - + +
4360D PRO 3.5 0.2 + - - -
4363D LEU* 1.3 74.6 - - + +
4365D SER* 1.3 70.2 + - - +
4366D TYR* 3.4 17.0 + - + -
4388D LEU* 3.8 41.7 - - + -
4425D MET* 6.3 0.2 - - - -
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Residues in contact with SER4365 (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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2B COA 4.4 24.9 + - - -
2361B MET* 5.3 4.4 - - - +
2365B SER* 2.7 40.0 + - - +
4D COA 4.4 10.4 + - - -
4305D SER* 4.2 7.2 + - - -
4306D LEU* 4.5 4.2 - - - +
4360D PRO 3.1 4.6 + - - -
4361D MET* 3.3 6.6 + - - +
4363D LEU 3.2 7.3 + - - -
4364D MET* 1.3 81.4 - - - +
4366D TYR* 1.3 65.4 + - - +
4367D PRO* 3.5 7.1 - - - +
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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
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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