Contacts of the helix formed by residues 98 - 114 (chain A) in PDB entry 3RIE
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 98 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 4.8 1.3 - - + -
94A LEU* 5.2 0.2 - - - -
95A THR* 2.9 20.7 + - - +
97A LYS* 1.3 83.5 - - + +
99A GLU* 1.4 67.1 + - - +
100A PHE* 3.1 9.6 - - + -
101A ALA* 3.0 23.4 + - + +
261A ILE* 3.4 16.9 - - + +
262A PRO* 3.3 23.3 - - + +
263A THR* 2.6 47.7 + - - +
601A GOL 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.0 13.2 - - + +
95A THR 3.1 21.9 + - - +
96A GLU* 4.3 10.1 - - - +
97A LYS 3.8 0.4 - - - -
98A ASP* 1.4 80.7 + - - +
100A PHE* 1.3 74.0 + - - +
101A ALA 3.1 0.9 + - - -
102A TYR* 3.2 5.4 + - - +
103A HIS* 2.5 64.8 + - + +
132A ARG* 2.8 40.5 + - - -
163A ILE* 3.9 24.1 - - + +
261A ILE* 4.6 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU 5.0 3.6 - - - -
97A LYS 3.2 27.1 - - - -
98A ASP* 3.1 6.0 + - + -
99A GLU* 1.3 93.4 + - - +
101A ALA* 1.4 77.4 + - + +
103A HIS 4.5 0.2 - - - +
104A GLU* 2.8 48.8 + - + +
132A ARG* 4.3 9.0 - - - +
297A LYS* 3.5 54.7 - - + +
298A TYR* 3.8 17.5 - + + -
601A GOL 3.8 35.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP* 3.0 14.5 + - + +
100A PHE* 1.4 89.6 - - + +
102A TYR* 1.3 64.6 + - - +
105A MET* 3.2 30.7 + - - +
259A ILE* 3.8 4.2 - - + +
260A SER 3.7 19.3 - - - +
261A ILE* 4.7 3.4 - - + -
298A TYR* 3.4 31.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP 4.0 0.4 + - - -
99A GLU* 3.2 7.0 + - - +
101A ALA* 1.3 82.9 - - - +
103A HIS* 1.3 83.5 + + - +
106A MET* 3.0 58.7 + - + +
130A ILE* 4.9 0.4 - - + -
196A ASP* 2.8 34.3 + - - -
229A GLN* 3.3 34.4 - - + +
259A ILE* 4.1 10.5 - - + +
261A ILE* 3.9 19.4 - - + +
264A TYR* 3.8 23.8 - + + +
269A ILE* 3.8 20.9 - - + -
270A GLY 5.7 0.4 - - - -
501A JFQ 3.6 16.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.0 9.0 - - + -
99A GLU* 2.5 60.1 + - + +
100A PHE 4.4 0.2 - - - +
102A TYR* 1.3 90.4 - + - +
104A GLU* 1.3 62.8 + - - +
107A THR* 2.8 30.8 + - - -
127A ASP* 3.4 14.4 + - - -
129A GLY* 3.8 22.1 - - - +
130A ILE* 3.7 27.9 - - + +
132A ARG* 4.2 6.5 - - - +
133A GLU* 4.0 3.8 - - + -
163A ILE* 4.8 0.4 - - + -
501A JFQ 2.9 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 2.8 34.8 + - + +
101A ALA 4.5 1.1 - - - +
103A HIS* 1.3 73.1 - - - +
105A MET* 1.3 55.4 + - - +
108A HIS* 2.9 43.1 + - + +
133A GLU* 3.8 23.4 - - - +
136A LYS* 5.2 1.0 + - - -
295A ASP 4.5 0.7 - - - +
296A LEU* 3.5 16.7 - - + +
297A LYS* 2.7 33.6 + - - +
298A TYR* 2.8 24.8 + - + -
299A TYR* 2.8 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA 3.2 20.4 + - - +
103A HIS 3.4 0.2 - - - -
104A GLU* 1.3 74.7 - - - +
106A MET* 1.3 63.2 + - - +
109A VAL* 3.2 51.7 + - + +
258A ASN 5.3 0.7 - - - +
259A ILE* 3.6 24.9 - - + -
271A ILE* 4.2 5.5 - - + +
298A TYR* 3.4 38.4 - - + -
299A TYR* 3.7 24.9 - - + -
303A ASN* 4.2 14.4 - - - +
304A HIS* 4.5 1.8 - - - -
307A ALA* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 3.0 59.7 + - + +
105A MET* 1.3 77.5 - - - +
107A THR* 1.3 56.6 + - - +
110A PRO* 3.0 22.9 - - - +
130A ILE* 3.7 13.5 - - + -
194A ILE* 3.9 21.1 - - + +
195A VAL 3.4 26.9 - - - +
196A ASP* 4.3 2.7 - - + -
227A VAL* 3.4 12.1 - - + +
228A ALA* 4.2 2.9 - - - -
229A GLN* 3.6 15.3 - - - +
259A ILE* 4.2 4.3 - - + -
270A GLY 5.2 0.2 - - - +
271A ILE* 3.9 31.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A HIS 2.8 22.1 + - - -
104A GLU 4.2 0.2 - - - -
106A MET* 1.3 76.6 - - - +
108A HIS* 1.3 69.6 + - + +
109A VAL 3.3 0.4 - - - -
110A PRO* 3.2 5.0 - - - +
111A MET* 3.0 34.1 + - + +
130A ILE* 3.4 22.5 - - - +
133A GLU* 3.6 27.8 - - + +
134A LEU* 3.4 36.3 - - + +
137A TYR* 4.5 0.2 - - + -
194A ILE* 4.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 2.9 34.1 + - + +
107A THR* 1.3 76.2 - - + +
109A VAL* 1.3 58.8 + - - +
111A MET 3.9 0.4 - - - -
112A THR* 2.6 35.7 + - - +
133A GLU* 2.9 44.7 + - + +
137A TYR* 2.7 44.6 + + - +
288A LEU* 4.0 4.5 - - + -
293A PHE* 3.8 10.3 - + - -
296A LEU* 3.7 14.8 - - + +
299A TYR* 3.0 34.2 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A MET* 3.2 47.9 + - + +
108A HIS* 1.3 82.4 - - - +
110A PRO* 1.4 69.6 - - + +
112A THR* 3.3 9.0 + - - -
113A VAL* 3.4 7.6 - - - +
227A VAL* 4.6 8.5 - - + -
271A ILE* 4.7 8.1 - - + -
273A CYS* 4.7 2.2 - - - -
281A LEU* 4.0 14.8 - - + +
299A TYR* 4.1 7.6 - - + -
304A HIS* 3.3 35.9 - - + +
307A ALA* 5.7 0.4 - - + -
308A PHE* 4.2 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET 3.0 28.9 - - - +
107A THR 3.2 8.5 - - - +
109A VAL* 1.4 93.8 - - + +
111A MET* 1.3 55.0 + - - +
113A VAL* 3.2 2.8 + - - +
114A SER* 2.9 30.0 + - - -
192A VAL* 4.0 26.7 - - + +
194A ILE* 4.3 2.2 - - + -
225A TYR* 4.5 9.3 - - + -
227A VAL* 3.8 28.9 - - + +
281A LEU* 3.8 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 3.0 28.7 + - + +
110A PRO* 1.3 76.9 - - + +
112A THR* 1.3 60.5 + - - +
114A SER* 3.8 4.3 - - - +
117A PRO* 3.6 25.4 - - + +
120A VAL* 3.8 18.2 - - + -
134A LEU* 3.7 25.6 - - + -
137A TYR* 3.3 38.7 - - + +
140A VAL* 3.6 26.7 - - + -
192A VAL* 3.9 21.1 - - + -
194A ILE* 5.1 0.4 - - + -
286A LYS* 2.8 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A HIS 2.6 20.4 + - - +
109A VAL 3.3 6.8 + - - -
111A MET* 1.3 77.2 - - - +
113A VAL* 1.3 54.5 + - - +
137A TYR* 4.0 2.9 - - - +
284A PRO* 3.5 8.9 - - - +
285A ASN* 2.7 36.4 + - - +
286A LYS* 3.5 26.9 + - + +
288A LEU* 3.8 29.8 - - + -
299A TYR* 2.7 29.6 + - + +
304A HIS* 3.3 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL 3.4 15.0 - - - +
110A PRO 3.2 2.4 + - - +
112A THR* 1.3 80.0 - - - +
114A SER* 1.3 63.3 + - - +
115A LYS* 3.3 3.8 + - - +
225A TYR* 3.7 30.7 + - + +
280A GLY 3.7 11.4 - - - +
281A LEU* 3.6 33.4 - - + +
283A LYS 3.6 16.8 - - - +
284A PRO* 4.1 0.2 - - + -
285A ASN* 2.9 31.0 + - - +
304A HIS* 3.5 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO 2.9 17.1 + - - -
111A MET* 3.8 0.8 - - - +
113A VAL* 1.3 74.5 - - - +
115A LYS* 1.3 57.1 + - - +
116A GLU 4.4 1.0 + - - -
117A PRO* 3.5 27.4 - - - +
191A ASP* 4.0 9.5 + - - +
192A VAL* 3.8 20.4 - - - +
223A ASN 5.5 0.7 + - - -
225A TYR* 4.0 16.6 - - - -
286A LYS* 2.6 35.7 + - - -
----------------------------------------------------------
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