Contacts of the helix formed by residues 92 - 105 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G GLU 3.1 11.1 + - - +
89G MET 3.2 13.2 - - - +
90G LEU 3.1 1.5 - - - -
91G LYS* 1.3 73.1 - - - +
93G GLU* 1.3 61.6 + - - +
94G VAL* 3.2 11.4 + - - +
95G ARG* 3.1 25.6 + - + +
96G THR* 3.1 25.1 + - - -
332G TYR* 4.1 8.8 - - + +
333G THR* 3.6 12.8 - - - -
334G HIS* 2.8 47.1 + - + +
335G TRP* 3.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LYS* 3.0 17.9 + - - +
92G ASP* 1.3 69.2 + - - +
94G VAL* 1.3 60.0 + - + +
97G LEU* 2.8 54.8 + - + +
243H TYR* 3.6 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ASP* 3.2 7.0 + - - +
93G GLU* 1.3 77.4 - - + +
95G ARG* 1.3 63.1 + - - +
97G LEU* 4.7 0.8 - - - +
98G THR* 2.7 33.3 + - - +
324G PHE* 3.5 31.6 - - + -
325G SER 5.1 1.8 - - - +
331G PRO* 4.4 24.2 - - + +
332G TYR 3.7 20.2 - - - +
333G THR* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G MET* 3.1 32.8 + - - +
90G LEU* 4.1 6.1 - - - +
92G ASP* 3.1 19.9 + - - +
94G VAL* 1.3 83.3 - - - +
96G THR* 1.3 88.5 + - - +
98G THR* 3.6 1.6 - - - -
99G TYR* 3.0 40.7 + - + -
124G ILE* 4.7 1.8 - - - +
125G LEU* 5.6 2.5 - - - +
185G GLU* 3.0 25.8 + - - +
324G PHE* 4.4 10.9 - - + -
333G THR* 5.4 0.2 - - - +
334G HIS* 3.6 14.8 - - - -
335G TRP* 3.5 33.4 - - + -
401G SAH 2.9 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G MET 3.2 6.4 + - - -
90G LEU* 3.3 5.8 + - + -
92G ASP 3.1 11.4 + - - -
95G ARG* 1.3 103.8 + - - +
97G LEU* 1.3 58.6 + - - +
99G TYR* 3.2 8.0 + - - +
100G ARG* 2.8 26.2 + - - +
124G ILE* 4.4 7.2 - - + -
125G LEU* 5.6 1.8 - - + -
128G PHE* 3.8 19.6 - - + -
243H TYR* 3.2 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G GLU* 2.8 43.0 + - + +
94G VAL* 4.7 0.4 - - - +
96G THR* 1.3 70.7 - - - +
98G THR* 1.3 58.1 + - - +
100G ARG* 3.3 40.8 - - - +
101G ASN* 2.9 42.1 + - - +
243H TYR* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G VAL* 2.7 27.0 + - - +
95G ARG 3.6 2.7 - - - -
97G LEU* 1.3 73.0 - - - +
99G TYR* 1.3 65.8 + - - +
101G ASN* 3.1 6.7 + - - +
102G SER* 2.9 22.7 + - - -
315G PHE* 3.6 27.4 - - + -
322G MET* 4.0 10.1 - - + +
323G GLY 3.8 26.4 + - - +
324G PHE* 3.8 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ARG* 3.0 35.9 + - + -
96G THR* 3.5 8.5 - - - +
98G THR* 1.3 74.7 - - - +
100G ARG* 1.3 62.6 + - - +
102G SER* 2.8 22.8 + - - -
103G MET* 3.5 19.3 + - + +
125G LEU* 3.6 40.4 - - + -
128G PHE* 4.4 1.3 - - - -
183G ILE* 5.5 0.4 - - + -
184G SER 2.6 30.5 + - - -
185G GLU* 3.3 22.7 - - + +
187G MET* 3.5 17.8 - - + +
215G PHE* 3.9 14.1 - - + -
216G PRO* 3.3 13.6 - - + +
315G PHE* 4.0 22.2 - + - -
324G PHE* 4.6 5.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G THR 2.8 15.7 + - - +
97G LEU* 3.3 33.5 - - + +
98G THR 3.2 0.2 - - - -
99G TYR* 1.3 72.8 - - - +
101G ASN* 1.3 73.4 + - - +
103G MET* 2.9 8.0 + - - +
104G TYR* 2.8 60.9 + - + +
128G PHE* 3.5 48.8 - - + -
243H TYR* 4.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G LEU* 2.9 26.8 + - - +
98G THR* 3.7 0.7 - - - +
100G ARG* 1.3 97.3 - - - +
102G SER* 1.3 66.5 + - - +
104G TYR* 4.4 2.3 - - - +
105G HIS* 3.0 60.5 + - + +
106G ASN* 4.1 0.5 - - - +
322G MET* 3.7 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G THR 2.9 14.1 + - - -
99G TYR* 2.8 16.5 + - - -
101G ASN* 1.3 78.2 - - - +
103G MET* 1.3 61.3 + - - +
106G ASN* 2.9 22.7 - - - +
215G PHE* 3.3 29.0 - - - -
315G PHE* 3.7 29.8 - - - -
318G CYS* 3.9 11.4 - - - -
322G MET* 3.6 10.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G TYR* 3.6 20.4 - - + +
100G ARG 2.9 4.9 + - - +
102G SER* 1.3 86.3 - - - +
104G TYR* 1.3 64.5 + - + +
105G HIS 3.2 1.6 - - - -
106G ASN 2.8 29.5 + - - -
107G LYS* 3.2 3.8 + - - -
110G PHE* 3.6 30.5 - - + -
125G LEU* 3.8 30.1 - - + +
128G PHE* 3.8 9.6 - - + +
129G ALA* 3.7 31.0 - - - -
132G ALA* 4.0 15.7 - - + +
183G ILE* 3.8 24.7 - - + -
215G PHE* 4.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345E TYR* 2.8 16.1 + - - -
100G ARG* 2.8 63.3 + - + +
101G ASN* 4.6 1.1 - - - +
103G MET* 1.3 75.1 - - + +
105G HIS* 1.3 69.8 + - + +
106G ASN 3.3 1.0 + - - -
107G LYS* 3.2 33.2 + - - +
128G PHE* 3.5 41.6 - - - -
131G LYS* 3.6 26.2 - - + +
132G ALA* 4.7 4.9 - - + -
243H TYR 4.9 2.1 + - - -
245H PHE* 3.8 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E ARG* 4.6 26.9 + - - -
303E TYR* 2.7 50.8 + + + +
345E TYR* 3.5 17.5 + + - -
347E THR* 5.2 0.3 + - - -
101G ASN* 3.0 51.2 + - + +
104G TYR* 1.3 86.2 - - + +
106G ASN* 1.3 63.4 + - - +
107G LYS 3.8 0.9 - - - -
108G HIS* 4.6 1.4 + - - -
322G MET* 4.8 10.5 - - + +
----------------------------------------------------------
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