Contacts of the helix formed by residues 4188 - 4205 (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 ASN4188 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4176D GLY 4.0 7.2 + - - -
4177D PHE* 4.0 13.1 + - - +
4187D GLY* 1.3 72.7 - - - +
4189D TRP* 1.3 64.5 + - - +
4190D GLY 3.1 3.6 - - - -
4191D HIS* 3.0 20.5 + - + -
4192D LEU* 3.0 14.7 + - + +
4320D GLY 4.0 1.8 + - - +
4321D THR* 3.3 11.6 - - - +
4322D VAL* 2.7 49.3 + - - +
4324D ASP* 3.2 25.2 + - - +
4327D LEU* 3.7 23.0 - - + +
4328D LEU* 5.0 0.4 - - - +
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Residues in contact with TRP4189 (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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4065D PHE* 3.2 40.9 - + - +
4066D THR* 3.5 27.1 - - - -
4067D PRO* 3.7 16.2 - - + -
4171D ARG* 3.8 19.1 + - - +
4175D TRP 3.6 18.4 - - - +
4176D GLY* 2.9 16.8 + - - +
4177D PHE 4.1 0.9 - - - -
4178D PHE 3.1 23.2 + - - -
4183D GLU 6.1 0.2 - - - -
4185D SER* 3.6 15.6 + - - -
4186D ARG* 3.7 15.7 - - + -
4187D GLY* 3.1 33.7 + - - -
4188D ASN* 1.3 72.6 - - - +
4190D GLY* 1.3 57.6 + - - +
4192D LEU* 3.3 15.5 + - + +
4193D ASP* 3.0 33.3 + - - +
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Residues in contact with GLY4190 (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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4170D TYR* 3.3 8.5 - - - +
4171D ARG 3.6 23.8 - - - -
4176D GLY 2.9 10.9 + - - -
4177D PHE* 3.8 10.3 - - - -
4188D ASN 3.1 0.6 - - - -
4189D TRP* 1.3 75.4 - - - +
4191D HIS* 1.3 63.1 + - - +
4193D ASP* 3.3 9.1 + - - -
4194D GLN* 3.2 26.8 + - - +
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Residues in contact with HIS4191 (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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4144D LEU* 4.5 2.0 - - + +
4177D PHE* 3.5 28.2 - + - -
4188D ASN* 3.0 10.5 + - - +
4190D GLY* 1.3 74.6 - - - +
4192D LEU* 1.3 61.9 + - - +
4194D GLN* 3.0 27.7 + - - +
4195D VAL* 3.0 30.4 + - - +
4225D GLU* 3.6 11.4 - - - -
4226D SER* 3.5 25.5 + - - -
4229D VAL* 4.6 7.1 - - + +
4230D LEU* 4.5 2.6 - - + +
4321D THR* 2.6 44.2 + - + +
4327D LEU* 3.3 30.7 - - + -
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Residues in contact with LEU4192 (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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4067D PRO* 4.1 22.0 - - + -
4068D PRO* 3.6 16.2 - - + +
4187D GLY 4.5 4.5 - - - +
4188D ASN* 3.0 16.6 + - + +
4189D TRP* 3.5 36.1 - - + +
4190D GLY 3.2 0.2 - - - -
4191D HIS* 1.3 76.7 - - - +
4193D ASP* 1.3 60.5 + - - +
4195D VAL* 3.3 7.7 + - + +
4196D ALA* 2.9 26.5 + - - +
4235D LEU* 3.7 31.0 - - + -
4324D ASP* 5.3 4.5 - - - +
4326D MET* 5.4 4.9 - - + -
4327D LEU* 4.5 14.1 - - + +
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Residues in contact with ASP4193 (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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4055D PHE* 3.4 13.4 - - + -
4068D PRO* 3.3 17.9 - - - +
4117D LEU* 3.6 19.0 - - + +
4169D GLN 5.1 0.2 - - - -
4170D TYR* 3.9 11.0 - - + -
4171D ARG* 2.9 61.3 + - - +
4189D TRP 3.0 11.5 + - - +
4190D GLY* 3.5 6.9 - - - +
4191D HIS 3.2 0.2 - - - -
4192D LEU* 1.3 75.6 - - - +
4194D GLN* 1.3 60.5 + - - +
4196D ALA* 3.2 1.7 + - - -
4197D ALA* 2.8 26.9 + - - +
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Residues in contact with GLN4194 (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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4139D ILE* 3.6 14.9 - - + +
4168D ILE* 4.0 23.1 - - + +
4170D TYR* 3.5 34.4 - - + -
4177D PHE* 5.6 0.2 - - - -
4190D GLY 3.2 12.3 + - - +
4191D HIS* 3.0 30.3 + - - +
4193D ASP* 1.3 78.4 - - - +
4195D VAL* 1.3 60.8 + - - +
4197D ALA* 3.3 3.5 + - - +
4198D LEU* 3.0 29.4 + - - +
4226D SER* 3.0 34.2 + - - -
4230D LEU* 4.3 17.9 - - + +
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Residues in contact with VAL4195 (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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4191D HIS 3.0 17.2 + - - +
4192D LEU* 3.5 11.4 - - + +
4194D GLN* 1.3 77.4 - - - +
4196D ALA* 1.3 58.5 + - - +
4198D LEU* 3.1 10.3 + - - +
4199D ARG* 2.9 28.9 + - + +
4230D LEU* 3.7 22.2 - - + -
4235D LEU* 4.0 26.2 - - + +
4236D ALA* 4.7 6.3 - - + -
4239D LEU* 3.8 17.1 - - + +
4327D LEU* 4.4 12.3 - - + -
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Residues in contact with ALA4196 (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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4055D PHE* 4.1 19.7 - - + +
4056D ALA* 5.1 0.9 - - + -
4068D PRO* 3.7 22.4 - - + +
4192D LEU 2.9 16.7 + - - +
4193D ASP* 3.2 6.0 + - - +
4195D VAL* 1.3 78.5 - - - +
4197D ALA* 1.3 62.1 + - - +
4199D ARG* 3.2 9.4 + - - +
4200D TRP* 2.9 22.0 + - - +
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Residues in contact with ALA4197 (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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4055D PHE* 3.8 28.0 - - + -
4119D LEU* 4.4 3.2 - - + +
4168D ILE* 3.9 34.5 - - + -
4193D ASP 2.8 20.0 + - - +
4194D GLN 3.6 5.4 - - - +
4196D ALA* 1.3 71.2 - - - +
4198D LEU* 1.3 58.6 + - + +
4200D TRP* 3.1 5.4 + - - +
4201D VAL* 2.9 31.8 + - - +
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Residues in contact with LEU4198 (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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4137D VAL* 4.1 28.3 - - + -
4139D ILE* 5.7 1.6 - - + -
4168D ILE* 5.7 1.6 - - + -
4194D GLN 3.0 19.9 + - - +
4195D VAL* 3.5 9.2 - - - +
4197D ALA* 1.3 73.6 - - + +
4199D ARG* 1.3 64.9 + - - +
4201D VAL* 3.3 6.3 + - + +
4202D GLN* 3.0 23.4 + - - +
4215D VAL* 4.4 3.1 - - + -
4217D ILE* 3.6 29.6 - - + -
4230D LEU* 4.0 27.6 - - + -
4236D ALA* 5.3 0.4 - - + -
4239D LEU* 4.0 40.6 - - + +
4240D PHE* 4.6 5.6 - - + -
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Residues in contact with ARG4199 (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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4195D VAL* 2.9 15.4 + - + +
4196D ALA* 3.5 12.1 - - - +
4198D LEU* 1.3 73.2 - - - +
4200D TRP* 1.3 67.5 + - - +
4202D GLN* 3.2 23.9 + - - +
4203D ASP* 2.9 59.1 + - - +
4238D ASN* 5.5 3.2 + - - +
4239D LEU* 4.2 20.7 - - + +
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Residues in contact with TRP4200 (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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4028D THR* 4.4 9.0 + - + -
4030D HIS* 4.7 17.2 - + - -
4053D ILE* 3.8 25.5 - - + +
4054D PRO 4.0 8.9 + - - -
4055D PHE* 3.8 33.0 - - + +
4074D TRP* 6.1 1.8 - + - -
4119D LEU* 3.7 20.0 - - + -
4121D ILE* 3.7 22.9 - - + -
4196D ALA 2.9 12.7 + - - +
4197D ALA 3.3 9.4 - - - +
4199D ARG* 1.3 78.2 - - - +
4201D VAL* 1.3 68.4 + - + +
4203D ASP* 3.1 3.3 + - - -
4204D ASN* 2.8 77.1 + - + +
4205D ILE* 4.7 6.5 - - + -
4208D PHE* 3.7 23.6 - + - -
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Residues in contact with VAL4201 (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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4119D LEU* 4.7 1.6 - - + -
4135D VAL* 4.3 8.3 - - + -
4137D VAL* 4.3 20.9 - - + -
4166D VAL* 4.5 18.6 - - + -
4197D ALA* 2.9 21.6 + - + +
4198D LEU* 3.5 11.2 - - + +
4199D ARG 3.2 0.2 - - - -
4200D TRP* 1.3 91.8 - - + +
4202D GLN* 1.3 58.5 + - - +
4205D ILE* 2.9 58.6 + - + +
4215D VAL* 4.1 22.0 - - + -
4239D LEU 6.1 0.2 - - - +
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Residues in contact with GLN4202 (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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4198D LEU 3.0 12.5 + - - +
4199D ARG* 3.2 35.4 + - - +
4201D VAL* 1.3 78.8 - - - +
4203D ASP* 1.3 62.0 + - - +
4204D ASN 3.7 0.2 + - - -
4205D ILE 4.7 0.5 + - - -
4206D ALA* 5.5 1.4 + - - +
4212D PRO* 3.1 53.3 + - + +
4213D GLY* 5.1 0.8 - - - -
4215D VAL* 4.1 10.4 - - - +
4238D ASN* 3.3 26.4 + - - +
4239D LEU* 4.2 9.8 - - + +
4241D HIS* 4.6 4.4 + - - -
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Residues in contact with ASP4203 (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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4029D VAL* 3.7 18.3 - - + +
4199D ARG* 2.9 59.8 + - - +
4200D TRP* 4.5 1.7 - - - -
4202D GLN* 1.3 78.4 - - - +
4204D ASN* 1.3 72.2 + - - +
4206D ALA* 5.6 1.0 - - - +
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Residues in contact with ASN4204 (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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4028D THR* 3.3 10.3 - - - -
4029D VAL* 2.9 40.2 + - - +
4030D HIS* 4.7 1.5 + - - -
4200D TRP* 2.8 74.9 + - + +
4203D ASP* 1.3 86.4 - - - +
4205D ILE* 1.3 64.4 + - - +
4206D ALA* 3.2 3.8 - - - -
4207D SER* 3.0 25.8 + - - -
4208D PHE* 3.6 5.9 - - + -
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Residues in contact with ILE4205 (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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4121D ILE* 4.3 13.2 - - + -
4135D VAL* 3.7 21.1 - - + -
4164D VAL* 4.1 19.5 - - + -
4166D VAL* 4.1 16.8 - - + -
4200D TRP* 4.3 4.9 + - + -
4201D VAL* 2.9 40.9 + - + +
4202D GLN 4.7 0.2 + - - -
4204D ASN* 1.3 72.4 - - - +
4206D ALA* 1.3 66.6 + - - +
4208D PHE* 2.8 24.7 + - + -
4209D GLY 3.4 0.2 + - - -
4210D GLY* 3.0 24.4 + - - +
4211D ASN 4.1 0.9 - - - -
4212D PRO* 3.7 33.0 - - + -
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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