Contacts of the strand formed by residues 4047 - 4054 (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 VAL4047 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4036D LYS 3.5 0.9 - - - +
4037D PHE* 3.3 4.0 - - - -
4038D VAL* 2.7 37.4 + - - +
4040D LEU 5.8 1.3 - - - +
4045D GLN 4.6 4.0 - - - +
4046D PRO* 1.3 75.9 - - + +
4048D ALA* 1.3 66.8 + - - +
4049D ILE* 3.5 11.5 + - + +
4122D TYR* 4.0 10.3 - - + -
4123D THR 3.4 28.9 - - - +
4124D PRO* 4.2 13.2 - - + -
4155D LEU* 3.5 33.0 - - + +
4158D ALA* 4.6 3.1 - - + -
4159D ALA* 4.1 21.3 - - + +
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Residues in contact with ALA4048 (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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4024D PRO* 4.1 5.2 - - + -
4036D LYS 3.5 5.4 - - - -
4037D PHE* 3.9 22.5 - - + -
4046D PRO 4.0 1.6 + - - -
4047D VAL* 1.3 70.3 - - - +
4049D ILE* 1.3 61.2 + - - +
4050D PHE* 3.8 14.8 - - + -
4121D ILE 3.6 2.6 - - - +
4122D TYR* 3.7 0.9 - - - -
4123D THR* 2.9 52.5 + - + +
4125D ALA 5.4 1.8 - - - +
4127D LEU* 3.9 11.7 - - + -
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Residues in contact with ILE4049 (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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4035D GLY* 3.3 4.5 - - - -
4036D LYS* 2.8 52.2 + - + +
4038D VAL* 3.5 32.3 - - + -
4047D VAL* 3.9 11.7 - - + +
4048D ALA* 1.3 78.0 - - - +
4050D PHE* 1.3 64.5 + - - +
4051D LEU* 3.7 29.4 - - + -
4080D ALA 4.1 1.2 - - - +
4121D ILE 3.3 4.3 - - - +
4122D TYR* 3.8 35.0 - - + -
4153D ASP* 5.1 0.7 - - - +
4155D LEU* 4.6 11.9 - - + -
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Residues in contact with PHE4050 (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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4024D PRO* 3.9 21.5 - - + -
4026D VAL* 3.6 24.2 - - + -
4033D VAL* 3.8 22.9 - - + -
4034D LEU 4.1 2.9 - - - -
4035D GLY* 3.5 29.6 - - - -
4048D ALA* 3.8 28.0 - - + -
4049D ILE* 1.3 74.0 - - - +
4051D LEU* 1.3 62.9 + - - +
4053D ILE* 3.7 21.0 - - + +
4080D ALA* 3.6 4.9 - - + -
4119D LEU 4.3 0.5 - - - +
4120D ASN* 3.3 5.2 - - - +
4121D ILE* 2.8 47.3 + - + +
4123D THR* 4.3 3.6 - - + -
4127D LEU* 4.3 0.9 - - + -
4208D PHE* 3.6 29.2 - + - -
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Residues in contact with LEU4051 (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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482D SIA 2.7 20.1 + - - -
4036D LYS* 4.4 16.4 - - - +
4049D ILE* 3.7 24.2 - - + -
4050D PHE* 1.3 74.8 - - - +
4052D GLY* 1.3 60.1 + - - +
4053D ILE 3.6 0.7 - - - -
4080D ALA* 2.8 28.9 + - - +
4081D THR* 3.9 23.1 - - - +
4082D SER 3.4 15.5 - - - +
4083D TYR* 3.7 46.7 - - + +
4120D ASN* 3.3 19.1 - - + +
4122D TYR* 3.9 9.0 - - - +
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Residues in contact with GLY4052 (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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482D SIA 2.8 39.4 + - - -
4051D LEU* 1.3 73.9 - - - +
4053D ILE* 1.3 63.0 + - - +
4054D PRO* 3.5 2.1 - - - +
4078D LYS* 4.8 0.7 - - - +
4080D ALA* 5.0 0.7 - - - +
4084D PRO* 3.8 16.9 - - - +
4118D TYR* 3.3 11.5 - - - -
4119D LEU 3.5 2.4 + - - -
4120D ASN* 2.7 17.6 + - - -
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Residues in contact with ILE4053 (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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4033D VAL* 4.5 19.7 - - + -
4050D PHE* 3.7 30.7 - - + +
4052D GLY* 1.3 73.7 - - - +
4054D PRO* 1.3 77.2 - - + +
4055D PHE 3.5 0.5 + - - -
4074D TRP* 4.9 4.7 - - + -
4078D LYS* 5.3 1.1 - - - -
4080D ALA* 4.4 11.4 - - + -
4118D TYR* 3.2 2.3 - - - -
4119D LEU* 2.9 43.3 + - + +
4121D ILE* 3.9 16.8 - - + -
4200D TRP* 3.8 24.5 - - + +
4208D PHE* 3.9 24.5 - - + -
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Residues in contact with PRO4054 (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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482D SIA 3.7 13.9 - - + -
4030D HIS* 5.3 0.5 - - - -
4052D GLY 3.5 8.9 - - - +
4053D ILE* 1.3 95.7 - - + +
4055D PHE* 1.3 60.8 + - - +
4056D ALA 3.5 13.5 - - - +
4058D PRO* 6.3 1.8 - - + -
4071D ALA* 4.1 11.8 - - + +
4074D TRP* 4.0 15.8 - - + -
4078D LYS* 3.8 24.5 - - + +
4117D LEU 3.6 8.5 - - - +
4118D TYR* 3.7 15.9 - - + -
4200D TRP* 4.0 6.6 + - - -
6183F GLU* 4.8 3.6 - - - +
6184F HIS* 6.1 4.5 - - + +
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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