Contacts of the helix formed by residues 4374 - 4385 (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 ASP4374 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2461B PRO* 3.9 3.8 - - - +
2462B LYS* 3.4 42.2 + - + -
4373D LEU* 1.3 75.7 - - - +
4375D GLN* 1.3 66.6 + - - +
4376D LYS* 3.4 15.0 + - - +
4377D THR* 2.5 49.6 + - - -
4378D ALA* 2.9 11.2 + - - +
4404D LEU* 5.2 0.2 - - - -
4410D THR* 4.8 3.8 - - - +
4413D LYS* 3.9 7.9 - - - -
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Residues in contact with GLN4375 (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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4374D ASP* 1.3 71.9 - - - +
4376D LYS* 1.3 57.2 + - - +
4378D ALA* 3.0 9.7 + - - +
4379D MET* 2.7 44.9 + - + +
4397D PRO 5.5 0.4 + - - -
4400D THR* 4.3 9.1 - - + +
4401D GLU* 3.5 30.6 + - - +
4404D LEU* 3.6 10.6 - - + +
4405D GLY* 2.8 34.2 + - - +
4407D THR 5.0 0.2 - - - +
4408D ASP* 5.3 0.9 - - - +
4413D LYS* 3.3 24.9 + - - +
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Residues in contact with LYS4376 (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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2452B ARG* 5.8 4.4 - - - +
2456B SER 5.5 1.2 + - - -
2457B SER 5.0 1.4 + - - -
2458B ASP* 2.7 45.8 + - - +
2460B LYS 5.9 0.8 + - - -
2462B LYS* 4.4 21.1 - - + +
4374D ASP* 3.2 12.8 + - - +
4375D GLN* 1.3 77.7 - - - +
4377D THR* 1.3 62.9 + - - +
4379D MET* 3.6 20.8 + - + +
4380D SER* 3.0 27.5 + - - +
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Residues in contact with THR4377 (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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2458B ASP 3.5 19.0 + - - +
2459B MET* 3.4 28.7 - - - +
2460B LYS 3.9 2.6 + - - -
2461B PRO* 3.9 11.5 - - - +
2462B LYS* 4.6 1.0 + - - +
4373D LEU* 3.7 21.3 - - + -
4374D ASP* 2.5 38.8 + - - -
4376D LYS* 1.3 76.8 - - - +
4378D ALA* 1.3 66.2 + - - +
4380D SER* 3.2 3.3 + - - -
4381D LEU* 3.0 25.1 + - + +
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Residues in contact with ALA4378 (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* 4.6 10.3 - - + +
4374D ASP 2.9 9.5 + - - +
4375D GLN 3.3 8.1 - - - +
4377D THR* 1.3 78.3 - - - +
4379D MET* 1.3 56.7 + - - +
4381D LEU* 3.3 2.3 + - - -
4382D LEU* 2.8 31.7 + - - +
4400D THR* 3.9 6.5 - - + -
4404D LEU* 3.3 34.8 - - + -
4417D PHE* 3.5 20.3 - - + -
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Residues in contact with MET4379 (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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4375D GLN* 2.7 26.3 + - + +
4376D LYS* 3.8 30.1 - - + +
4378D ALA* 1.3 71.7 - - - +
4380D SER* 1.3 62.1 + - - +
4382D LEU* 3.3 2.4 + - - +
4383D TRP* 3.0 23.7 + - - +
4396D ILE* 3.7 18.6 - - + +
4397D PRO* 3.9 33.7 - - - +
4400D THR* 3.5 23.1 - - + +
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Residues in contact with SER4380 (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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2458B ASP* 3.3 38.7 + - - +
2459B MET* 4.6 6.3 - - - -
4376D LYS* 3.0 14.7 + - - +
4377D THR 3.2 9.3 + - - -
4379D MET* 1.3 77.6 - - - +
4381D LEU* 1.3 57.4 + - - +
4383D TRP* 3.3 8.6 + - - +
4384D LYS* 3.0 32.7 + - - +
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Residues in contact with LEU4381 (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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2459B MET* 3.8 36.1 - - + +
4306D LEU* 5.0 4.0 - - + +
4366D TYR* 5.2 3.8 - - + -
4367D PRO* 4.1 25.4 - - + +
4368D LEU* 3.9 19.7 - - + -
4373D LEU* 3.9 33.0 - - + -
4377D THR* 3.0 21.6 + - + +
4378D ALA 3.8 0.9 - - - +
4380D SER* 1.3 73.4 - - - +
4382D LEU* 1.3 56.6 + - - +
4384D LYS* 3.2 8.8 + - + +
4385D SER* 2.7 37.1 + - - +
4417D PHE* 3.7 16.6 - - + -
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Residues in contact with LEU4382 (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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4378D ALA 2.8 18.1 + - - +
4379D MET* 3.6 5.6 - - - +
4380D SER 3.3 0.2 - - - -
4381D LEU* 1.3 76.0 - - - +
4383D TRP* 1.3 63.3 + - - +
4385D SER* 3.2 16.3 + - - -
4386D TYR* 3.6 5.4 + - - -
4389D VAL* 4.0 13.6 - - + +
4391D ILE* 4.0 33.4 - - + +
4396D ILE* 4.0 18.4 - - + +
4399D ALA* 4.2 12.3 - - + -
4400D THR* 3.5 22.2 - - - +
4417D PHE* 4.0 17.4 - - + -
4420D LEU* 4.3 21.3 - - + -
4421D ILE* 4.5 9.2 - - + -
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Residues in contact with TRP4383 (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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4311D ASP* 3.9 18.4 + - - -
4312D PRO* 3.2 41.1 - - + +
4313D ARG* 3.6 33.4 - - + -
4379D MET 3.0 10.3 + - - +
4380D SER* 3.5 11.7 - - - +
4381D LEU 3.2 0.2 - - - -
4382D LEU* 1.3 75.6 - - - +
4384D LYS* 1.3 73.3 + - + +
4386D TYR* 3.0 38.3 + + - +
4391D ILE 3.7 3.6 - - - -
4392D ALA* 5.3 0.2 - - - -
4393D LYS* 3.5 64.8 - - + +
4396D ILE* 3.3 28.9 - - + +
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Residues in contact with LYS4384 (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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2459B MET* 4.1 27.4 - - - -
4306D LEU* 3.5 19.5 - - + +
4307D ASP 4.2 17.5 + - - +
4308D LEU* 3.4 37.0 + - + -
4310D GLY 3.3 26.1 + - - +
4312D PRO* 4.1 17.5 - - + +
4315D SER* 5.3 0.9 + - - -
4380D SER* 3.0 20.6 + - - +
4381D LEU* 3.2 10.3 + - + +
4383D TRP* 1.3 81.6 - - + +
4385D SER* 1.3 56.7 + - - +
4386D TYR 3.1 3.6 + - - -
4387D PRO* 3.5 10.6 - - - +
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Residues in contact with SER4385 (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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4306D LEU* 4.2 4.3 - - - +
4366D TYR* 2.9 37.2 + - - -
4381D LEU 2.7 21.3 + - - -
4382D LEU* 3.5 13.4 - - - -
4383D TRP 3.0 0.6 - - - -
4384D LYS* 1.3 75.1 - - - +
4386D TYR* 1.3 63.8 + - - +
4387D PRO* 3.2 5.2 - - - -
4388D LEU* 2.8 18.2 + - - +
4389D VAL* 3.0 18.3 + - - +
4421D ILE* 4.3 11.3 - - - +
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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