Contacts of the helix formed by residues 98 - 114 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B TRP* 3.6 28.0 - - + -
82C TYR* 4.6 1.8 - - + -
94C LEU* 5.3 0.3 - - - -
95C THR* 2.7 27.8 + - - +
97C LYS* 1.3 77.6 - - + +
99C GLU* 1.4 70.2 + - - +
100C PHE* 3.1 5.2 - - - -
101C ALA* 2.9 21.9 + - - +
261C ILE* 3.5 12.4 - - + +
262C PRO* 3.4 13.1 - - + +
263C THR* 2.4 46.6 + - - +
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Residues in contact with GLU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 4.0 13.5 - - + -
95C THR 3.1 22.0 + - - +
96C GLU* 4.0 10.5 - - - +
97C LYS 3.7 0.6 - - - -
98C ASP* 1.4 79.1 + - - +
100C PHE* 1.3 74.6 + - - +
101C ALA 3.1 1.0 + - - -
102C TYR* 3.3 4.8 + - - +
103C HIS* 2.8 62.2 + - + +
132C ARG* 2.8 40.1 + - - -
162C ASN* 5.8 0.7 - - - +
163C ILE* 3.8 23.0 - - + +
261C ILE* 4.6 5.8 - - - -
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Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B TRP* 3.6 27.1 - + - -
313B PHE* 3.8 15.9 - + - -
96C GLU 5.2 2.5 - - - -
97C LYS 3.1 27.4 - - - -
98C ASP* 4.1 2.5 - - - -
99C GLU* 1.3 94.2 + - - +
101C ALA* 1.3 77.5 + - - +
103C HIS 4.0 0.7 - - - +
104C GLU* 3.0 45.6 + - + +
132C ARG* 4.3 9.0 - - - +
297C LYS* 3.5 52.3 - - + -
298C TYR* 3.7 17.9 - + + -
601C GOL 3.9 18.2 - - - -
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B TRP* 4.0 9.2 - - + -
98C ASP 2.9 13.9 + - - +
100C PHE* 1.3 84.1 - - - +
102C TYR* 1.3 63.9 + - - +
104C GLU* 4.4 0.2 - - - +
105C MET* 3.2 30.5 + - - +
259C ILE* 3.7 4.7 - - + +
260C SER 3.4 19.5 - - - +
261C ILE* 4.4 4.0 - - + -
298C TYR* 3.3 33.7 - - + -
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Residues in contact with TYR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLU* 3.3 5.8 + - - +
101C ALA* 1.3 82.3 - - - +
103C HIS* 1.3 81.6 + + - +
104C GLU 3.3 0.2 + - - -
105C MET* 3.3 0.7 + - - -
106C MET* 3.0 59.5 + - + +
130C ILE* 4.9 0.4 - - + -
196C ASP* 2.5 36.2 + - - -
229C GLN* 3.4 25.5 - - + +
259C ILE* 4.2 10.1 - - + -
261C ILE* 3.8 20.5 - - + +
264C TYR* 3.7 25.1 - + + +
269C ILE* 3.8 20.2 - - + -
270C GLY 5.7 0.4 - - - -
501C JFQ 3.2 24.0 + - - -
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Residues in contact with HIS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 4.2 7.4 - - + -
99C GLU* 2.8 51.1 + - + +
102C TYR* 1.3 88.2 - + - +
104C GLU* 1.3 61.0 + - - +
107C THR* 2.7 32.2 + - - -
127C ASP* 3.4 15.6 + - - -
129C GLY* 3.7 32.0 - - - +
130C ILE* 3.8 19.6 - - + +
132C ARG* 4.1 3.4 - - - +
133C GLU* 3.8 8.0 - - + +
163C ILE* 4.6 1.1 - - + -
501C JFQ 2.9 34.3 + - - -
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C PHE* 3.0 37.8 + - + +
101C ALA 4.4 0.9 - - - +
103C HIS* 1.3 78.3 - - - +
105C MET* 1.4 57.4 + - - +
108C HIS* 2.8 45.2 + - + +
133C GLU* 3.6 24.5 - - - +
136C LYS* 5.2 1.4 + - - -
295C ASP 4.3 1.7 - - - +
296C LEU* 3.6 17.6 - - + +
297C LYS* 2.9 24.3 + - - +
298C TYR* 2.7 26.5 + - + -
299C TYR* 2.9 20.5 + - + +
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Residues in contact with MET 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ALA 3.2 19.1 + - - +
104C GLU* 1.4 74.5 - - - +
106C MET* 1.3 65.0 + - - +
109C VAL* 3.2 49.6 + - + +
258C ASN 5.3 0.7 - - - +
259C ILE* 3.7 26.0 - - + -
271C ILE* 3.8 5.3 - - + +
298C TYR* 3.5 36.8 - - + -
299C TYR* 3.7 22.0 - - - -
303C ASN* 3.8 14.6 - - - +
304C HIS* 4.2 4.0 - - - -
307C ALA* 3.7 29.8 - - + -
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Residues in contact with MET 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 3.0 62.6 + - + +
105C MET* 1.3 77.5 - - - +
107C THR* 1.3 59.1 + - - +
110C PRO* 3.2 18.9 - - - +
130C ILE* 3.7 13.7 - - + -
194C ILE* 3.9 21.2 - - + +
195C VAL 3.6 24.5 - - - +
196C ASP* 4.1 4.9 - - + -
227C VAL* 3.4 14.2 - - + +
228C ALA* 4.3 2.9 - - - +
229C GLN* 3.7 12.8 - - - +
259C ILE* 4.5 3.4 - - + -
270C GLY 5.1 0.4 - - - +
271C ILE* 4.0 33.2 - - - +
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Residues in contact with THR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C HIS 2.7 22.8 + - - -
104C GLU 4.1 0.9 - - - -
106C MET* 1.3 76.7 - - - +
108C HIS* 1.3 69.6 + - + +
109C VAL 3.3 0.2 - - - -
110C PRO* 3.3 5.4 - - - +
111C MET* 3.1 35.0 + - + +
130C ILE* 3.5 18.4 - - - +
133C GLU* 3.5 29.9 - - + +
134C LEU* 3.6 38.1 - - + +
137C TYR* 4.4 0.2 - - + -
194C ILE* 4.2 6.5 - - + -
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Residues in contact with HIS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU* 2.8 37.7 + - + +
107C THR* 1.3 77.9 - - + +
109C VAL* 1.3 56.9 + - - +
111C MET 4.0 0.4 - - - -
112C THR* 2.7 37.1 + - - +
133C GLU* 2.9 43.3 + - + +
136C LYS* 4.8 0.2 - - + -
137C TYR* 2.8 41.8 + + - -
288C LEU* 3.5 14.3 - - + +
293C PHE* 3.8 13.0 - + - -
296C LEU* 3.6 18.8 - - + +
299C TYR* 3.6 22.5 + - + -
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C MET* 3.2 48.2 + - + +
108C HIS* 1.3 79.7 - - - +
110C PRO* 1.3 72.0 - - + +
112C THR* 3.5 2.9 + - - -
113C VAL* 3.5 6.4 - - - +
227C VAL* 4.8 0.9 - - + -
257C ALA* 5.6 0.7 - - + -
271C ILE* 4.4 8.7 - - + -
273C CYS* 4.5 10.3 - - - -
281C LEU* 3.9 17.5 - - + +
299C TYR* 4.0 2.4 - - + -
304C HIS* 3.2 44.2 - - + +
308C PHE* 3.9 18.4 - - + -
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Residues in contact with PRO 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C MET 3.2 26.2 - - - +
107C THR 3.3 9.9 - - - +
109C VAL* 1.3 91.1 - - + +
111C MET* 1.3 59.0 + - - +
113C VAL* 2.9 17.7 + - - +
114C SER* 3.0 18.6 + - - -
192C VAL* 4.0 25.1 - - + -
194C ILE* 4.2 2.7 - - + -
225C TYR* 4.6 8.0 - - + -
227C VAL* 3.7 25.8 - - + +
281C LEU* 3.6 19.4 - - + +
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Residues in contact with MET 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C THR* 3.1 18.8 + - + +
110C PRO* 1.3 77.6 - - + +
112C THR* 1.3 58.8 + - - +
114C SER* 3.5 3.6 - - - +
117C PRO* 3.5 26.9 - - + +
120C VAL* 3.9 7.4 - - + -
134C LEU* 3.7 31.0 - - + -
137C TYR* 3.2 43.9 - - + +
140C VAL* 3.5 26.2 - - + -
192C VAL* 3.9 27.4 - - - -
194C ILE* 5.0 0.9 - - + -
286C LYS* 2.9 26.9 + - - +
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C HIS 2.7 23.5 + - - +
111C MET* 1.3 77.0 - - - +
113C VAL* 1.3 61.2 + - - +
137C TYR* 3.7 14.6 - - - +
284C PRO* 3.6 3.0 - - - +
285C ASN* 2.8 27.4 + - - +
286C LYS* 3.6 29.2 + - + +
288C LEU* 3.8 26.7 - - + -
299C TYR* 3.1 21.3 + - - +
304C HIS* 3.3 15.6 + - - -
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C VAL 3.5 13.9 - - - +
110C PRO 2.9 6.7 + - - +
112C THR* 1.3 80.4 - - - +
114C SER* 1.3 66.7 + - - +
115C LYS* 3.4 3.1 + - - +
225C TYR* 3.6 24.3 + - + +
279C THR* 6.0 0.2 - - - +
280C GLY 3.5 22.0 - - - +
281C LEU* 3.7 27.8 - - + +
283C LYS 3.5 20.2 - - - +
285C ASN* 2.7 36.3 + - - +
304C HIS* 3.8 8.5 - - + -
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Residues in contact with SER 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PRO 3.0 14.7 + - - -
111C MET 3.5 1.4 - - - +
113C VAL* 1.3 78.5 - - - +
115C LYS* 1.3 54.8 + - - +
116C GLU 4.3 0.7 + - - -
117C PRO* 3.5 27.0 - - - +
191C ASP* 4.3 6.8 + - - +
192C VAL* 4.1 14.4 - - - +
223C ASN 5.7 0.2 + - - -
225C TYR* 3.8 27.7 - - - -
286C LYS* 2.7 32.1 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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