Contacts of the helix formed by residues 91 - 110 (chain C) in PDB entry 3OMA
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 ASN 91 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C MET* 2.9 22.6 + - - +
64C CYS 4.3 1.6 + - - -
65C ALA* 4.0 16.3 - - + +
68C LEU* 3.8 20.4 - - - +
90C PRO* 1.3 71.0 - - - +
92C GLY* 1.3 63.0 + - - +
93C HIS 3.2 7.6 + - - -
94C LEU* 3.2 28.7 + - + +
95C TRP 3.7 2.4 + - - -
165C GLN* 2.7 44.3 + - - +
484C ILE* 3.2 15.3 - - - +
258D ILE* 3.9 4.7 - - - +
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Residues in contact with GLY 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PRO* 3.8 4.4 + - - +
91C ASN* 1.3 74.0 + - - +
93C HIS* 1.3 61.3 + - - +
95C TRP* 3.2 4.2 + - - +
96C ASN* 3.1 30.0 + - - +
484C ILE* 3.9 22.9 - - - +
258D ILE* 3.5 27.8 + - - +
262D TYR* 5.3 3.4 - - - -
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Residues in contact with HIS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ASN* 3.1 1.6 + - - -
92C GLY* 1.3 76.6 - - - +
94C LEU* 1.3 59.0 + - - +
96C ASN* 3.3 8.2 + - - +
97C VAL* 2.9 38.1 + - + +
162C GLY* 3.3 18.7 + - - -
163C ASN* 3.1 16.7 + - - +
165C GLN* 3.5 46.2 - - + +
166C LEU 3.2 14.1 + - - -
167C GLY 3.0 28.2 + - - -
169C GLY* 3.8 6.0 + - - -
182C GLU* 3.4 17.0 + - - -
258D ILE* 3.5 15.7 - - + +
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 4.5 12.6 - - + +
62C PHE 5.5 0.2 - - - +
63C MET* 3.8 36.1 - - + -
64C CYS 5.7 2.0 - - - +
67C HIS* 6.3 0.7 - - + -
79C SER* 5.6 4.9 - - - -
91C ASN* 3.2 28.3 + - - +
93C HIS* 1.3 76.9 - - - +
95C TRP* 1.3 65.8 + - - +
97C VAL* 3.3 10.9 + - + +
98C MET* 2.9 48.9 + - + +
165C GLN* 5.1 0.4 - - - +
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Residues in contact with TRP 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 2.9 26.6 + - + -
51C MET* 3.4 37.9 - - + -
54C GLU* 3.9 13.7 - - + -
55C LEU* 3.3 37.7 - - + -
63C MET* 3.5 31.7 - - + -
91C ASN 3.7 1.4 + - - -
92C GLY 3.2 9.8 + - - +
94C LEU* 1.3 79.6 - - - +
96C ASN* 1.3 74.8 + - - +
98C MET* 3.3 0.9 + - - +
99C ILE* 3.0 48.7 + - + +
482C ARG* 3.7 12.4 - - - -
483C TYR 3.5 14.1 + - - -
484C ILE* 3.6 35.4 - - + -
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Residues in contact with ASN 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLY* 3.1 17.6 + - - +
93C HIS* 3.7 8.0 + - - +
95C TRP* 1.3 90.7 - - - +
97C VAL* 1.3 54.6 + - - +
99C ILE* 3.8 6.5 - - - +
100C THR* 2.6 36.9 + - - -
169C GLY* 3.4 25.2 + - - +
482C ARG* 3.7 12.0 - - - +
484C ILE* 5.6 0.5 + - - +
255D LEU* 3.7 16.1 - - + +
257D GLY 3.0 35.6 + - - -
258D ILE* 4.0 4.8 - - - +
260D HIS* 5.2 1.1 - - - +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C HIS* 2.9 46.4 + - + +
94C LEU* 3.7 10.8 - - + +
96C ASN* 1.3 74.3 - - - +
98C MET* 1.3 65.9 + - - +
100C THR* 3.4 1.9 + - - -
101C GLY* 2.9 27.0 + - - -
157C LEU* 3.9 27.3 - - + +
166C LEU 3.7 5.2 - - - +
167C GLY* 3.5 27.1 - - - -
168C SER 3.6 13.8 - - - +
169C GLY 3.7 0.7 - - - +
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Residues in contact with MET 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 3.7 55.9 - - + +
50C TYR* 4.1 19.7 - - + -
51C MET* 4.3 16.2 - - + -
63C MET* 4.1 16.2 - - + -
94C LEU* 2.9 42.0 + - + +
95C TRP* 3.6 4.7 - - - +
97C VAL* 1.3 77.9 - - - +
99C ILE* 1.3 53.5 + - + +
101C GLY* 3.2 2.0 + - - -
102C HIS* 2.7 37.2 + - - +
157C LEU* 6.2 1.6 - - - -
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Residues in contact with ILE 99 (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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1C HEA 3.3 61.3 - - + +
51C MET* 3.5 29.8 - - + -
95C TRP* 3.0 52.7 + - + +
96C ASN* 3.8 11.0 - - - +
98C MET* 1.3 72.7 - - + +
100C THR* 1.3 64.9 + - - +
102C HIS* 3.5 2.7 + - - +
103C GLY 3.0 22.7 + - - -
171C GLY* 5.0 1.3 - - - -
482C ARG* 4.2 14.8 - - + +
255D LEU* 5.4 1.8 - - + -
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Residues in contact with THR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASN 2.6 22.5 + - - -
97C VAL 3.7 0.7 - - - -
99C ILE* 1.3 77.3 - - - +
101C GLY* 1.3 58.3 + - - +
103C GLY* 3.3 0.5 + - - -
104C ILE* 2.9 47.0 + - + +
168C SER* 3.5 20.6 - - - +
170C ILE* 3.3 10.8 + - + -
171C GLY* 2.8 42.7 + - - +
172C TRP* 4.3 7.7 - - - +
174C LEU* 5.2 2.0 - - + -
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Residues in contact with GLY 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 4.1 16.8 - - - -
97C VAL 2.9 15.0 + - - -
98C MET 3.5 3.1 - - - -
100C THR* 1.3 74.6 - - - +
102C HIS* 1.3 64.1 + - - +
104C ILE* 4.8 3.8 - - - -
105C LEU* 3.0 32.1 + - - +
157C LEU* 4.3 13.0 - - - +
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Residues in contact with HIS 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 2.1 85.3 + + + -
44C SER* 2.9 31.2 + - - +
47C PHE* 3.7 11.2 - - + -
48C THR* 3.0 29.4 - - + +
51C MET* 3.9 15.3 - - + -
98C MET 2.7 20.1 + - - +
99C ILE 3.7 4.3 - - - +
101C GLY* 1.3 70.4 - - - +
103C GLY* 1.3 61.2 + - - +
106C MET* 3.2 36.0 + - + +
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Residues in contact with GLY 103 (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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1C HEA 3.9 26.5 - - - -
99C ILE 3.0 15.6 + - - -
100C THR 3.7 2.5 - - - -
102C HIS* 1.3 75.1 - - - +
104C ILE* 1.3 65.8 + - - +
106C MET* 3.9 0.3 - - - +
107C MET* 3.0 30.2 + - - +
172C TRP* 3.9 12.8 - - - -
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Residues in contact with ILE 104 (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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100C THR* 2.9 32.6 + - + +
101C GLY* 4.1 4.0 - - - +
103C GLY* 1.3 70.3 - - - +
105C LEU* 1.3 64.6 + - + +
107C MET* 5.0 0.2 - - - -
108C PHE* 3.0 43.8 + - + +
109C PHE* 3.7 23.2 - - + -
153C ALA* 4.5 10.5 - - + -
172C TRP* 3.2 34.5 - - + +
174C LEU* 4.3 12.8 - - + -
190C ALA* 5.6 10.5 - - + +
193C ALA* 5.7 0.4 - - + -
194C VAL* 4.6 13.2 - - + -
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 3.9 22.7 - - + -
43C ILE* 4.3 10.8 - - + -
44C SER* 3.9 31.0 - - - +
47C PHE* 4.1 21.3 - - + -
101C GLY* 3.0 21.8 + - - +
104C ILE* 1.3 76.1 - - + +
106C MET* 1.3 56.8 + - - +
109C PHE* 2.8 44.8 + - + -
110C VAL* 3.0 11.6 + - - -
150C THR* 4.8 2.5 - - + -
153C ALA* 4.3 16.2 - - + -
154C VAL* 4.6 17.7 - - + -
157C LEU* 5.7 2.0 - - + -
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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
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1C HEA 3.5 81.7 - - + -
41C GLY 4.3 0.4 - - - +
44C SER* 3.4 26.9 - - - +
45C VAL* 3.9 16.6 - - + -
102C HIS* 3.2 32.3 + - + +
103C GLY 3.9 2.5 - - - +
105C LEU* 1.3 79.3 - - - +
107C MET* 1.3 62.9 + - - +
108C PHE 3.5 0.3 + - - -
110C VAL* 3.9 14.6 - - - -
111C VAL* 3.4 29.3 + - - +
112C ILE 4.9 0.2 + - - -
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Residues in contact with MET 107 (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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1C HEA 3.6 25.8 - - + -
2C HEA 4.2 9.4 - - + -
103C GLY 3.0 22.2 + - - +
106C MET* 1.3 79.8 - - - +
108C PHE* 1.3 66.3 + - + +
112C ILE* 3.8 12.6 - - - +
172C TRP* 3.8 42.8 - - + -
286C GLU* 2.6 44.1 - - + +
287C VAL* 4.2 4.3 - - + -
290C ILE* 3.8 17.2 - - + +
424C MET* 3.6 27.6 - - - +
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Residues in contact with PHE 108 (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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104C ILE* 3.0 28.9 + - + +
107C MET* 1.3 83.2 - - + +
109C PHE* 1.3 77.8 + - + +
110C VAL 3.8 1.6 - - - -
112C ILE* 5.4 1.8 - - + +
113C PRO* 3.5 18.9 - - - +
146C TYR* 4.7 0.9 - - - -
172C TRP* 4.0 24.9 - + - -
194C VAL* 3.9 28.5 - - + -
197C SER* 3.3 33.3 + - - +
243C LEU* 4.8 5.8 - - + -
246C LEU* 3.7 21.3 - - + -
282C PHE* 3.6 37.7 - + - -
286C GLU* 4.7 2.0 - - - -
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 3.4 21.9 - - + +
104C ILE* 3.7 26.2 - - + -
105C LEU* 2.8 29.5 + - + +
108C PHE* 1.3 82.3 - + + +
110C VAL* 1.3 60.7 + - - +
113C PRO* 3.7 5.8 - - - -
146C TYR* 2.9 34.0 + + - -
149C GLY* 3.4 15.0 - - - -
150C THR* 3.2 37.9 - - + +
153C ALA* 3.6 20.0 - - + -
193C ALA* 3.3 25.6 - - + -
194C VAL* 5.1 0.4 - - + -
197C SER* 3.6 22.2 - - - -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.9 27.8 - - + -
37C GLY* 3.6 20.3 - - - +
40C VAL* 3.6 9.0 - - + +
41C GLY* 3.5 33.7 - - - +
105C LEU* 3.0 23.1 + - + +
106C MET* 3.9 14.6 - - - +
109C PHE* 1.3 82.8 - - - +
111C VAL* 1.3 67.7 + - + +
113C PRO* 3.5 6.6 - - - +
114C ALA* 3.0 29.8 + - - +
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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