Contacts of the strand formed by residues 98 - 102 (chain C) in PDB entry 2HU4
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 ALA 98 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 6.0 2.9 - - + -
204B VAL* 4.3 14.4 - - + -
211B ILE* 3.8 21.6 - - + +
214B THR* 4.3 9.4 - - - +
97C TRP* 1.3 74.1 - - - +
99C VAL* 1.3 66.5 + - - +
100C TYR 3.3 0.2 + - - -
446C PHE* 3.3 2.7 - - - -
447C CYS 3.0 28.7 + - - +
448C GLY 4.1 0.4 + - - -
449C VAL* 4.0 20.4 - - + -
453C THR* 4.0 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER* 5.0 2.8 + - - -
176B VAL* 4.1 25.4 + - + +
195B SER* 4.7 11.4 - - - -
202B VAL* 5.5 7.9 - - + -
204B VAL* 4.0 21.9 - - + +
206B LYS* 4.7 1.7 - - - -
211B ILE* 3.7 10.0 - - - +
97C TRP 4.0 0.8 + - - +
98C ALA* 1.3 71.4 - - - +
100C TYR* 1.3 61.8 + - - +
101C SER 4.7 4.0 - - - +
102C LYS* 6.2 0.2 - - + -
444C ILE* 5.9 1.1 - - + -
445C SER 4.2 2.9 - - - +
446C PHE* 3.5 30.7 - - + -
458C TRP* 3.5 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 3.3 5.6 - - - -
175B SER* 4.5 0.5 - - - -
176B VAL* 4.6 3.1 - - - -
206B LYS* 2.8 40.1 + - - +
209B GLY 3.3 28.9 + - - -
210B ILE* 4.7 4.9 - - - +
211B ILE* 4.0 18.6 - - + -
98C ALA 3.3 1.5 + - - +
99C VAL* 1.3 74.8 - - - +
101C SER* 1.3 65.5 + - - +
122C ILE* 5.2 0.9 - - + -
129C CYS* 3.7 26.0 - - + +
163C VAL* 4.5 22.0 - - + +
410C PHE* 4.3 15.7 - + - -
412C GLN* 4.1 18.5 + - - -
445C SER* 2.7 35.9 + - - +
446C PHE* 3.9 10.5 - - - -
447C CYS* 4.1 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 3.3 24.0 - - - -
176B VAL* 3.6 8.0 - - - +
99C VAL* 3.9 2.8 - - - +
100C TYR* 1.3 87.1 - - - +
102C LYS* 1.3 64.0 - - - +
122C ILE* 4.5 5.2 - - - +
163C VAL* 4.7 3.9 - - - +
164C GLY* 4.2 15.1 + - - -
443C SER* 5.7 1.4 + - - -
444C ILE* 3.2 8.7 - - - +
445C SER* 2.5 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PRO 3.3 28.5 - - - +
155B HIS* 3.2 15.5 - - - -
157B THR* 3.8 10.6 + - + +
173B PHE* 3.6 20.0 - - - -
176B VAL* 3.7 13.7 - - + -
101C SER* 1.3 79.8 + - - +
103C ASP* 1.3 61.8 + - - +
104C ASN* 2.6 39.6 - - - +
164C GLY* 3.6 4.4 - - - +
426C LEU* 5.1 1.2 - - - +
442C SER* 5.8 1.6 - - - -
443C SER 3.5 7.4 - - - +
444C ILE* 3.7 21.6 - - + +
458C TRP* 4.4 11.0 - - + -
459C PRO 3.0 28.7 + - - -
460C ASP* 3.5 6.7 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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