Contacts of the helix formed by residues 4409 - 4426 (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 ASP4409 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4407D THR* 4.1 3.8 + - - -
4408D ASP* 1.3 72.5 - - - +
4410D THR* 1.3 52.4 + - - +
4411D VAL* 2.6 23.2 + - - +
4412D LYS* 2.4 71.2 + - + +
4413D LYS* 3.0 8.1 + - - +
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Residues in contact with THR4410 (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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2461B PRO* 6.1 0.2 - - - +
2463B THR* 5.2 9.0 - - + +
4372D GLN* 3.4 31.0 - - - +
4373D LEU 3.0 53.3 + - - +
4374D ASP* 4.4 3.6 + - - +
4408D ASP 2.6 13.2 + - - -
4409D ASP* 1.3 69.2 - - - +
4411D VAL* 1.3 67.8 + - + +
4413D LYS* 3.5 4.7 - - - +
4414D LYS 3.5 5.0 + - - -
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Residues in contact with VAL4411 (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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2370B GLU 4.1 7.2 - - - +
2371B GLY* 4.7 4.7 - - - -
2372B GLN* 3.9 21.3 - - - +
2411B VAL* 4.3 25.8 - - + -
4371D GLY 4.0 20.6 - - - +
4372D GLN* 4.0 12.1 - - - +
4409D ASP* 2.6 16.3 + - - +
4410D THR* 1.3 84.6 - - + +
4412D LYS* 1.3 63.6 + - + +
4414D LYS* 3.1 11.6 + - - +
4415D ASP* 3.0 25.1 + - - +
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Residues in contact with LYS4412 (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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4407D THR* 4.2 23.3 - - + +
4409D ASP* 2.4 58.5 + - + +
4411D VAL* 1.3 67.1 - - + +
4413D LYS* 1.3 51.9 + - - +
4415D ASP* 2.8 13.3 + - + +
4416D LEU* 2.8 42.6 + - + +
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Residues in contact with LYS4413 (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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4373D LEU* 3.1 29.4 - - - +
4374D ASP* 3.9 11.2 - - - +
4375D GLN* 3.3 36.6 + - + +
4404D LEU* 3.4 26.0 + - + +
4407D THR* 2.6 32.9 + - - +
4408D ASP* 3.0 26.9 + - - +
4409D ASP 3.0 8.8 + - - +
4410D THR* 3.5 9.0 - - - +
4412D LYS* 1.3 76.9 - - - +
4414D LYS* 1.3 55.7 + - - +
4416D LEU* 4.5 9.0 - - + +
4417D PHE* 2.8 30.9 + - - +
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Residues in contact with LYS4414 (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* 3.1 24.1 + - - +
2370B GLU* 2.9 47.4 + - - -
4368D LEU* 4.6 7.6 - - + -
4371D GLY* 3.9 13.2 - - - +
4372D GLN* 3.9 19.3 - - - +
4373D LEU* 4.0 21.1 - - + +
4410D THR 3.5 2.2 + - - -
4411D VAL 3.1 9.1 + - - +
4412D LYS 3.1 0.4 - - - -
4413D LYS* 1.3 79.8 - - - +
4415D ASP* 1.3 78.2 + - - +
4417D PHE* 3.3 7.8 + - - +
4418D LEU* 3.1 45.1 + - + +
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Residues in contact with ASP4415 (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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2370B GLU* 4.6 6.9 - - - +
2372B GLN* 4.8 5.1 + - - -
4353D GLN* 5.4 6.1 + - - -
4411D VAL* 3.0 26.6 - - - +
4412D LYS* 2.8 15.2 + - + +
4414D LYS* 1.3 98.6 + - - +
4416D LEU* 1.3 58.8 + - + +
4418D LEU* 3.2 8.1 + - - +
4419D ASP* 3.0 33.0 + - - +
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Residues in contact with LEU4416 (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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4403D TYR* 3.2 31.5 - - + +
4404D LEU* 3.4 23.6 - - + +
4406D GLY* 6.0 0.2 - - - -
4407D THR* 4.4 20.0 - - + +
4412D LYS* 2.8 29.1 + - + +
4413D LYS* 4.7 2.2 - - + -
4415D ASP* 1.3 71.7 - - + +
4417D PHE* 1.3 60.4 + - - +
4419D ASP* 3.2 19.0 + - + +
4420D LEU* 2.9 28.9 + - - +
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Residues in contact with PHE4417 (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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4366D TYR* 4.7 7.4 - + - -
4368D LEU* 4.8 5.6 - - + -
4373D LEU* 3.8 20.4 - - + -
4378D ALA* 3.5 34.8 - - + -
4381D LEU* 3.7 27.6 - - + -
4382D LEU* 4.0 21.3 - - + -
4385D SER* 4.7 1.1 - - - -
4400D THR* 5.9 0.7 - - + -
4404D LEU* 3.4 11.8 - - + +
4413D LYS 2.8 19.9 + - - +
4414D LYS* 3.3 7.9 - - + +
4415D ASP 3.2 0.2 - - - -
4416D LEU* 1.3 77.3 - - - +
4418D LEU* 1.3 75.1 + - + +
4420D LEU* 3.4 12.0 + - + +
4421D ILE* 3.2 50.4 + - + +
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Residues in contact with LEU4418 (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* 5.0 4.3 - - - +
2370B GLU* 4.6 0.4 - - - +
4353D GLN* 5.8 2.2 - - - +
4355D PHE* 3.5 52.1 + - + +
4356D GLY* 3.8 16.4 - - - +
4360D PRO* 4.9 1.8 - - + -
4368D LEU* 4.1 22.2 - - + -
4414D LYS* 3.1 48.2 + - + +
4415D ASP* 3.2 8.5 + - - +
4417D PHE* 1.3 86.5 - - + +
4419D ASP* 1.3 59.6 - - - +
4421D ILE 3.5 0.6 + - - +
4422D ALA* 3.0 28.2 + - - +
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Residues in contact with ASP4419 (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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4352D LYS 4.6 11.6 - - - +
4353D GLN* 5.0 11.1 + - - +
4403D TYR* 4.1 11.0 - - + -
4415D ASP* 3.0 20.3 + - - +
4416D LEU* 3.2 25.3 + - + +
4418D LEU* 1.3 74.4 - - - +
4420D LEU* 1.3 60.7 + - - +
4422D ALA* 3.3 5.8 + - - +
4423D ASP* 2.9 38.5 + - - +
4540D LYS* 6.2 1.8 - - - +
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Residues in contact with LEU4420 (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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4382D LEU* 4.3 28.3 - - + -
4389D VAL* 5.5 0.4 - - + -
4391D ILE* 4.4 0.4 - - + -
4399D ALA 3.8 27.8 - - - +
4400D THR* 4.3 8.1 - - + -
4403D TYR* 3.5 31.6 - - + -
4404D LEU* 5.2 1.8 - - + -
4416D LEU 2.9 15.1 + - - +
4417D PHE* 3.5 15.3 - - + +
4419D ASP* 1.3 77.0 - - - +
4421D ILE* 1.3 65.3 + - - +
4423D ASP* 3.2 3.6 + - - +
4424D VAL* 3.1 24.2 + - + +
4547D TRP* 3.2 30.2 - - + -
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Residues in contact with ILE4421 (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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4355D PHE* 3.7 46.4 - - + -
4366D TYR* 4.2 8.5 - - + +
4382D LEU* 4.5 10.1 - - + -
4385D SER* 4.3 7.6 - - - +
4388D LEU* 5.2 2.2 - - + -
4389D VAL* 4.2 21.3 - - + -
4417D PHE* 3.2 48.2 + - + +
4418D LEU 3.9 3.8 - - - +
4420D LEU* 1.3 76.2 - - + +
4422D ALA* 1.3 63.7 + - - +
4424D VAL* 3.3 2.4 + - - +
4425D MET* 3.0 37.6 + - - +
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Residues in contact with ALA4422 (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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4352D LYS 5.7 2.2 - - - +
4353D GLN* 5.1 2.0 - - - -
4354D GLU* 3.9 15.0 - - + +
4355D PHE* 3.9 25.1 - - - +
4418D LEU 3.0 19.4 + - - +
4419D ASP* 3.6 8.3 - - - +
4421D ILE* 1.3 76.7 - - - +
4423D ASP* 1.3 59.7 + - - +
4426D PHE* 2.8 36.7 + - - +
4427D GLY 3.1 7.0 + - - -
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Residues in contact with ASP4423 (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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4403D TYR* 2.5 38.0 + - - +
4419D ASP* 2.9 20.1 + - - +
4420D LEU 3.6 3.1 - - - +
4422D ALA* 1.3 79.2 - - - +
4424D VAL* 1.3 61.4 + - - +
4427D GLY* 3.5 5.4 + - - +
4428D VAL* 2.8 38.1 + - + +
4429D PRO* 3.4 1.2 - - - +
4540D LYS* 2.8 35.8 + - - +
4543D GLU* 3.3 17.8 - - - +
4547D TRP* 4.2 5.4 - - - +
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Residues in contact with VAL4424 (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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4252D THR* 5.6 0.5 - - - -
4253D SER* 5.6 4.8 + - - +
4388D LEU 5.0 0.4 - - - +
4389D VAL* 3.6 40.8 - - + +
4391D ILE* 4.5 1.8 - - + -
4420D LEU* 3.1 19.3 + - + +
4421D ILE 3.8 4.9 - - - +
4423D ASP* 1.3 76.6 - - - +
4425D MET* 1.3 57.9 + - - +
4428D VAL* 4.9 3.6 - - - -
4429D PRO* 3.1 21.7 - - - +
4547D TRP* 3.5 41.7 - - + -
4551D PHE* 4.5 14.6 - - + -
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Residues in contact with MET4425 (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 4.2 19.7 - - + -
4252D THR* 3.0 33.7 + - + +
4253D SER* 5.9 1.6 - - - +
4254D VAL* 3.8 28.7 - - + -
4355D PHE* 4.0 17.3 - - + -
4359D ILE* 5.5 1.8 - - + -
4364D MET* 6.3 0.2 - - - -
4388D LEU* 3.6 44.4 - - + +
4389D VAL* 4.4 1.8 - - + -
4421D ILE* 3.0 38.8 + - + +
4424D VAL* 1.3 78.1 - - - +
4426D PHE* 1.3 76.1 + - + +
4429D PRO* 3.6 6.6 - - - +
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Residues in contact with PHE4426 (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 3.9 28.7 - - - -
4221D SER* 4.6 1.1 - - - -
4247D SER* 3.2 36.3 - - - -
4248D GLY* 4.1 7.0 - - - -
4249D VAL* 6.1 0.2 - - - -
4252D THR* 4.6 6.5 - - + -
4255D LEU* 6.4 0.2 - - + -
4350D ILE* 4.2 7.4 - - + -
4354D GLU* 3.5 42.0 - - + -
4355D PHE* 5.1 2.2 - + - -
4359D ILE* 3.9 15.5 - - + -
4422D ALA* 2.8 17.0 + - - +
4424D VAL 3.6 0.4 - - - -
4425D MET* 1.3 101.9 - - + +
4427D GLY* 1.3 64.9 + - - +
4428D VAL 3.5 1.6 - - - -
4429D PRO* 3.6 2.4 - - - +
4430D SER* 2.7 33.9 + - - +
4468D HIS* 3.9 16.4 - + - -
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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