Contacts of the helix formed by residues 4090 - 4102 (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 ASP4090 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D COA 2.5 82.2 + - - +
4089D GLN* 1.3 74.2 - - - +
4091D PRO* 1.3 65.0 - - - +
4092D LYS* 3.0 15.1 + - - +
4093D ALA* 3.1 6.6 + - + +
4094D GLY* 2.8 27.9 + - - -
4145D MET 5.0 0.2 + - - -
4146D VAL* 4.4 2.5 - - + +
4295D LEU* 4.1 1.8 - - - +
4298D THR* 5.1 7.6 - - + +
4299D LEU* 4.0 18.8 - - + +
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Residues in contact with PRO4091 (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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4086D MET* 4.7 6.5 - - + +
4089D GLN 2.8 10.7 - - - +
4090D ASP* 1.3 87.2 - - - +
4092D LYS* 1.3 63.3 + - + +
4095D GLN* 3.0 30.0 + - - +
4112D LEU* 4.0 27.4 - - + -
4295D LEU* 4.4 13.9 - - + -
4299D LEU* 5.1 5.8 - - + -
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Residues in contact with LYS4092 (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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2300B LYS 2.7 29.2 + - - +
2301B MET* 3.3 11.1 + - - +
2302B LYS* 2.9 52.1 - - + +
2309B GLN* 3.4 19.7 + - - +
4D COA 3.7 17.3 - - + +
4090D ASP* 3.0 8.2 + - - +
4091D PRO* 1.3 79.5 - - + +
4093D ALA* 1.3 66.7 + - - +
4095D GLN* 3.3 2.4 + - - -
4096D LEU* 3.0 21.8 + - - +
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Residues in contact with ALA4093 (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 75.1 + - + +
4090D ASP* 3.1 12.7 + - + +
4092D LYS* 1.3 79.5 - - - +
4094D GLY* 1.3 62.8 + - - +
4096D LEU* 3.4 4.1 + - - +
4097D LEU 3.0 19.1 + - - -
4146D VAL* 4.1 2.7 - - + -
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Residues in contact with GLY4094 (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 0.7 - - - -
4086D MET* 4.6 9.0 - - - +
4089D GLN* 3.3 27.6 - - - -
4090D ASP 2.8 14.5 + - - -
4091D PRO 4.0 0.4 - - - -
4093D ALA* 1.3 77.3 - - - +
4095D GLN* 1.3 60.9 + - - +
4097D LEU* 3.4 2.6 + - - +
4098D SER* 3.1 23.6 + - - -
4146D VAL* 4.2 7.3 - - - +
4147D GLY* 4.9 2.8 + - - -
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Residues in contact with GLN4095 (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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2309B GLN* 2.6 32.7 + - - +
4086D MET* 4.6 5.9 - - + +
4091D PRO 3.0 19.3 + - - +
4092D LYS* 5.6 0.7 - - - -
4094D GLY* 1.3 75.8 - - - +
4096D LEU* 1.3 62.8 + - - +
4098D SER* 3.3 5.8 + - - -
4099D GLU* 3.0 34.3 + - - +
4107D ASN* 4.3 10.9 - - - +
4109D PRO* 4.6 22.1 - - + +
4110D LEU 5.7 0.9 - - - +
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Residues in contact with LEU4096 (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* 4.7 23.3 - - + +
2309B GLN* 3.3 19.4 + - + +
4D COA 4.0 26.5 - - + +
4092D LYS 3.0 18.2 + - - +
4093D ALA* 3.6 5.2 - - - +
4095D GLN* 1.3 77.7 - - - +
4097D LEU* 1.3 63.4 + - - +
4099D GLU* 3.2 10.9 + - + +
4100D LEU* 3.1 43.3 + - + +
4361D MET* 4.6 5.2 - - + -
4363D LEU* 3.8 24.2 - - + -
4459D MET* 5.7 3.6 - - + -
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Residues in contact with LEU4097 (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 55.2 + - - +
4093D ALA 3.0 8.8 + - - +
4094D GLY* 3.8 4.5 - - - +
4096D LEU* 1.3 77.7 - - - +
4098D SER* 1.3 63.4 + - - +
4100D LEU* 3.2 7.2 + - + -
4101D PHE* 2.9 60.4 + - + +
4141D GLY 4.1 7.2 - - - +
4142D GLY* 3.9 10.1 - - - +
4146D VAL* 3.8 12.3 - - + -
4147D GLY* 4.4 10.1 - - - -
4152D TYR* 5.6 1.6 - - - +
4358D LEU* 5.0 0.4 - - + -
4363D LEU* 4.6 6.5 - - + -
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Residues in contact with SER4098 (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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4086D MET* 6.1 1.8 - - - -
4094D GLY 3.1 18.4 + - - -
4095D GLN* 3.6 7.6 - - - -
4097D LEU* 1.3 77.2 - - - +
4099D GLU* 1.3 57.6 + - - +
4102D THR* 2.9 27.5 + - - -
4107D ASN* 2.8 33.1 + - - +
4108D ILE 4.8 3.7 + - - -
4110D LEU* 4.9 8.3 - - - +
4148D ALA* 6.1 0.7 - - - -
4151D THR* 2.8 34.5 + - - +
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Residues in contact with GLU4099 (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 5.3 1.2 - - - +
2309B GLN* 2.9 43.2 - - - +
4095D GLN* 3.0 19.6 + - - +
4096D LEU* 3.2 13.1 + - + +
4098D SER* 1.3 76.7 - - - +
4100D LEU* 1.3 64.1 + - + +
4102D THR* 3.7 12.3 - - - +
4107D ASN* 3.5 32.4 + - + +
4482D LYS* 5.0 4.0 + - - -
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Residues in contact with LEU4100 (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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4096D LEU* 3.1 38.9 + - + +
4097D LEU* 3.7 7.4 - - + +
4099D GLU* 1.3 80.2 - - + +
4101D PHE* 1.3 68.8 + - + +
4357D TRP* 4.9 3.6 - - + -
4358D LEU* 3.5 29.6 - - + -
4361D MET* 3.9 17.7 - - + -
4363D LEU* 4.4 4.3 - - + -
4455D PHE 5.2 1.4 - - - +
4457D SER* 3.6 33.4 - - - +
4459D MET* 5.5 3.4 - - + -
4473D PHE* 3.4 22.3 - - - -
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Residues in contact with PHE4101 (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 4.8 6.7 - - - -
4097D LEU* 2.9 41.6 + - + +
4100D LEU* 1.3 84.7 - - + +
4102D THR* 1.3 68.8 + - - +
4103D ASN* 3.5 2.8 + - - +
4141D GLY 5.8 3.1 - - - -
4151D THR* 4.1 5.6 - - + -
4152D TYR* 3.5 36.4 - - - +
4220D GLU* 3.8 21.8 - - - -
4358D LEU* 3.4 38.1 - - + -
4468D HIS* 4.1 5.2 - + - -
4469D GLY* 4.0 26.2 - - - -
4472D LEU* 3.8 19.8 - - + +
4473D PHE* 4.2 12.5 - + - -
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Residues in contact with THR4102 (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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4098D SER 2.9 20.8 + - - +
4099D GLU 3.7 12.3 - - - +
4100D LEU 3.7 0.2 - - - -
4101D PHE* 1.3 79.5 - - - +
4103D ASN* 1.3 51.4 + - - +
4104D ARG* 2.9 36.8 + - - +
4107D ASN* 3.6 26.4 + - + +
4151D THR* 2.7 28.1 + - - +
4152D TYR* 5.6 0.2 - - - +
4473D PHE* 3.5 2.9 - - - -
4482D LYS* 2.7 33.9 + - - +
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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