Contacts of the helix formed by residues 92 - 105 (chain K) in PDB entry 5DST
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 ASP 92 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K GLU 3.3 12.2 + - - +
89K MET 3.4 12.6 - - - +
90K LEU 3.1 1.9 - - - -
91K LYS* 1.3 73.3 - - - +
93K GLU* 1.3 62.3 + - - +
94K VAL* 3.3 11.6 + - - +
95K ARG* 3.2 25.5 + - + +
96K THR* 3.0 25.1 + - - -
332K TYR* 4.1 9.3 - - + +
333K THR* 3.6 13.9 - - - -
334K HIS* 2.9 47.2 + - + +
335K TRP* 4.0 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K LYS* 2.9 15.9 + - - +
92K ASP* 1.3 68.4 + - - +
94K VAL* 1.3 61.4 + - + +
97K LEU* 2.8 54.4 + - + +
243L TYR* 3.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K ASP* 3.3 8.1 + - - +
93K GLU* 1.3 81.1 - - + +
95K ARG* 1.3 63.7 + - - +
97K LEU* 5.1 0.4 - - - -
98K THR* 3.0 28.9 + - - +
324K PHE* 3.6 30.9 - - + -
325K SER 5.1 1.3 - - - +
331K PRO* 4.4 23.8 - - + +
332K TYR 3.7 18.8 - - - +
333K THR* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K MET* 2.9 41.9 + - - +
90K LEU* 4.0 8.3 - - - +
92K ASP* 3.2 19.9 + - - +
94K VAL* 1.3 84.3 - - - +
96K THR* 1.3 80.5 + - - +
98K THR* 3.7 1.7 - - - -
99K TYR* 3.1 41.6 + - + -
124K ILE* 4.7 1.8 - - - +
125K LEU* 5.6 2.5 - - - +
185K GLU* 3.1 25.6 - - - +
324K PHE* 4.5 9.6 - - + -
334K HIS* 3.7 15.5 - - - -
335K TRP* 3.6 32.3 - - + -
401K SAH 2.8 38.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K MET 3.1 18.0 + - - -
90K LEU* 3.3 6.5 + - + +
92K ASP 3.0 16.0 + - - -
95K ARG* 1.3 90.4 + - - +
97K LEU* 1.3 62.0 + - - +
99K TYR* 3.4 7.0 + - + +
100K ARG* 2.9 26.6 + - - +
124K ILE* 4.4 7.4 - - + -
125K LEU* 5.7 1.8 - - + -
128K PHE* 3.8 18.5 - - + -
243L TYR* 3.4 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93K GLU* 2.8 44.8 + - + +
94K VAL* 4.7 0.7 - - - +
96K THR* 1.3 71.6 - - - +
98K THR* 1.3 59.1 - - - +
100K ARG* 3.5 37.7 - - - +
101K ASN* 2.8 40.1 + - - +
243L TYR* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94K VAL* 3.0 23.0 + - - +
95K ARG 3.7 2.7 - - - -
96K THR 3.3 0.6 - - - -
97K LEU* 1.3 75.4 - - - +
99K TYR* 1.3 66.3 + - - +
101K ASN* 4.7 3.8 - - - -
102K SER* 2.9 23.2 + - - -
315K PHE* 3.5 31.0 - - + -
322K MET* 3.8 11.4 - - + +
323K GLY 3.8 23.4 + - - +
324K PHE* 3.9 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K ARG* 3.1 41.1 + - + -
96K THR* 3.7 9.4 - - - +
98K THR* 1.3 75.8 - - - +
100K ARG* 1.3 61.6 + - - +
102K SER* 2.6 23.5 + - - -
103K MET* 3.4 21.4 - - + +
125K LEU* 3.7 34.1 - - + -
128K PHE* 4.4 1.8 - - + -
183K ILE* 5.5 0.2 - - + -
184K SER 2.6 34.8 + - - -
185K GLU* 3.3 22.2 - - + -
187K MET* 3.5 16.6 - - + +
215K PHE* 4.0 12.8 - - + -
216K PRO* 3.3 13.6 - - + +
315K PHE* 4.0 22.7 - + - -
324K PHE* 4.7 4.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K THR 2.9 18.3 + - - +
97K LEU* 3.5 32.2 - - + +
98K THR 3.2 0.2 - - - -
99K TYR* 1.3 74.2 - - - +
101K ASN* 1.3 78.4 + - - +
103K MET* 3.0 4.0 + - - +
104K TYR* 2.9 63.1 + - + +
128K PHE* 3.4 46.4 - - + -
243L TYR* 4.4 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K LEU* 2.8 30.1 + - - +
98K THR* 4.7 0.6 - - - -
100K ARG* 1.3 96.6 - - - +
102K SER* 1.3 57.9 + - - +
104K TYR* 4.7 1.3 - - - +
105K HIS* 2.8 71.7 + - + +
322K MET* 3.8 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K THR 2.9 16.2 + - - -
99K TYR* 2.6 23.9 + - - -
101K ASN* 1.3 74.8 - - - +
103K MET* 1.3 63.6 + - - +
106K ASN* 2.9 22.8 - - - +
215K PHE* 3.5 21.4 - - - -
315K PHE* 3.9 20.7 - - - -
318K CYS* 3.9 19.5 - - - -
322K MET* 3.7 10.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K TYR* 3.4 24.9 - - + +
100K ARG 3.0 4.8 + - - +
102K SER* 1.3 80.8 - - - +
104K TYR* 1.3 71.4 + - + +
105K HIS 3.2 1.3 - - - -
106K ASN 3.0 22.7 + - - +
107K LYS 3.3 1.6 + - - -
110K PHE* 3.6 31.8 - - + -
125K LEU* 3.9 21.8 - - + +
128K PHE* 3.8 9.4 - - + +
129K ALA* 3.6 31.9 - - - -
132K ALA* 3.8 17.4 - - + +
183K ILE* 3.9 29.6 - - + -
215K PHE* 4.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345I TYR* 2.8 17.0 + - - -
100K ARG* 2.9 58.7 + - + +
101K ASN* 4.7 0.9 - - - +
103K MET* 1.3 74.5 - - + +
105K HIS* 1.3 68.5 + - + +
106K ASN 3.3 0.7 + - - -
107K LYS* 3.3 32.8 + - - +
128K PHE* 3.4 44.5 - - - -
131K LYS* 3.5 25.3 - - + +
132K ALA* 4.6 5.4 - - + -
243L TYR 4.9 1.7 + - - -
245L PHE* 3.6 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I ARG* 4.7 24.0 + - - -
303I TYR* 2.5 51.2 + + + +
345I TYR* 3.7 15.1 + + - -
347I THR* 5.2 0.7 + - - -
101K ASN* 2.8 60.7 + - + +
104K TYR* 1.3 78.0 - - + +
106K ASN* 1.3 62.3 + - - +
107K LYS 3.8 0.9 - - - -
108K HIS* 4.8 1.4 + - - -
322K MET* 4.8 9.9 - - + +
----------------------------------------------------------
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