Contacts of the helix formed by residues 97 - 110 (chain C) in PDB entry 1EQB
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 SER 97 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C PRO* 3.1 1.9 - - - +
96C HIS* 1.3 82.6 - - - +
98C GLY* 1.3 62.1 + - - +
99C SER* 3.5 3.3 + - - -
100C GLN* 2.6 34.5 + - - +
101C ALA 3.0 21.8 + - - -
235C ARG 6.0 0.2 - - - -
236C GLY* 3.7 4.0 - - - -
237C GLY* 3.2 22.1 - - - +
3291C PLP 3.5 18.8 + - - -
96D HIS* 4.0 15.7 + - - -
263D GLY 5.4 0.2 - - - -
265D LEU* 6.1 0.7 - - - -
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Residues in contact with GLY 98 (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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97C SER* 1.3 72.6 - - - +
99C SER* 1.3 66.3 + - - +
101C ALA* 3.2 6.6 + - - +
102C ASN* 3.0 28.1 + - - +
225C THR 5.1 1.6 - - - -
226C THR* 3.5 19.0 - - - +
237C GLY* 4.5 1.8 - - - -
3291C PLP 3.3 32.1 + - - -
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Residues in contact with SER 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C SER* 4.0 3.4 - - - -
98C GLY* 1.3 76.2 - - - +
100C GLN* 1.3 58.0 + - - +
102C ASN* 3.3 3.4 + - - +
103C PHE* 2.8 29.5 + - - +
126C HIS* 4.5 1.4 - - - -
128C THR* 3.9 26.9 - - - +
135C PHE* 4.1 4.9 - - - -
3291C PLP 2.9 22.1 + - - -
260D GLY 4.0 7.0 - - - -
261D GLN* 3.5 13.2 - - - -
262D GLY* 3.1 22.6 + - - -
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Residues in contact with GLN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO* 4.4 1.7 - - - +
96C HIS* 4.0 5.8 - - + +
97C SER* 2.6 35.1 + - - +
98C GLY 3.2 0.6 - - - -
99C SER* 1.3 79.1 + - - +
101C ALA* 1.3 65.4 + - - +
103C PHE* 3.3 14.1 + - + +
104C ALA* 3.1 22.7 + - - +
256C VAL* 5.7 0.2 - - - +
261C GLN* 3.4 28.9 - - + +
96D HIS* 3.5 16.1 - - - -
100D GLN* 3.5 39.8 - - - +
103D PHE* 6.2 1.6 - - - -
260D GLY 3.1 23.4 + - - -
261D GLN* 4.0 3.8 - - - +
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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
----------------------------------------------------------
95C PRO* 3.8 23.5 - - + +
97C SER 3.0 19.0 + - - +
98C GLY* 3.6 6.3 - - - +
100C GLN* 1.3 74.5 - - - +
102C ASN* 1.3 63.8 + - - +
104C ALA* 3.2 14.6 + - - +
105C VAL* 3.2 15.9 + - - +
224C THR* 4.0 20.1 - - + +
225C THR 4.9 0.7 - - - +
237C GLY* 4.3 0.7 - - - -
238C LEU 4.0 17.0 - - - +
239C ILE* 4.2 3.6 - - + +
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Residues in contact with ASN 102 (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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98C GLY* 3.0 16.5 + - - +
99C SER 3.6 6.5 - - - +
101C ALA* 1.3 72.7 - - - +
103C PHE* 1.3 66.6 + - - +
105C VAL* 3.1 4.6 + - - +
106C TYR* 3.0 39.6 + - + -
128C THR* 2.7 32.0 + - - +
129C HIS* 4.3 3.2 + - - -
135C PHE* 4.9 0.2 - - + -
198C PHE* 3.3 16.1 - - + -
200C ASP* 2.9 21.7 + - - +
224C THR* 2.8 28.9 + - - -
3291C PLP 3.7 6.1 - - - -
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Residues in contact with PHE 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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99C SER 2.8 21.8 + - - +
100C GLN* 3.6 17.3 - - + +
102C ASN* 1.3 70.7 - - - +
104C ALA* 1.3 63.9 + - - +
106C TYR* 3.4 2.9 + - - +
107C THR* 2.9 56.5 + - + +
135C PHE* 3.5 43.7 - + + -
139C LEU* 4.6 8.1 - - + -
255C ALA 5.5 0.4 - - - -
259C GLY 5.2 0.9 - - - -
260C GLY* 4.3 26.2 - - - -
100D GLN* 6.3 0.9 - - - -
103D PHE* 3.6 39.5 - + - -
135D PHE* 4.5 12.3 - - + -
139D LEU* 5.2 3.1 - - + -
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Residues in contact with ALA 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 GLN 3.1 11.7 + - - +
101C ALA* 3.4 10.1 - - - +
102C ASN 3.1 0.2 - - - -
103C PHE* 1.3 81.4 - - + +
105C VAL* 1.3 62.8 + - - +
107C THR* 3.2 8.4 + - - -
108C ALA* 2.9 26.4 + - - +
239C ILE* 4.1 6.3 - - + -
252C LEU* 5.1 1.1 - - + +
255C ALA* 3.4 14.4 - - + +
256C VAL* 3.7 32.5 - - + +
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Residues in contact with VAL 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 3.6 4.3 - - - +
102C ASN 3.1 7.7 + - - +
104C ALA* 1.3 76.9 - - - +
106C TYR* 1.3 64.5 + - - +
108C ALA 3.4 0.2 + - - -
109C LEU* 3.2 35.4 + - + +
169C MET* 3.8 21.0 - - + +
198C PHE* 3.9 25.8 - - + -
222C VAL* 3.8 20.6 - - + -
224C THR* 3.5 31.9 - - + -
239C ILE* 4.7 4.5 - - + -
252C LEU* 4.4 13.2 - - + -
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Residues in contact with TYR 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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102C ASN* 3.0 40.2 + - + -
103C PHE* 3.6 6.7 - - - +
104C ALA 3.2 0.2 - - - -
105C VAL* 1.3 77.3 - - - +
107C THR* 1.3 60.0 + - + +
108C ALA 3.1 0.2 - - - -
110C LEU* 2.8 51.5 + - + +
116C VAL* 4.6 11.7 - - + -
128C THR 2.4 31.1 + - - -
129C HIS* 3.7 2.3 - - - -
130C GLY* 5.0 0.2 - - - -
135C PHE* 3.8 17.9 - + + -
136C SER* 3.6 11.3 - - - -
140C TYR* 3.5 41.3 - + + +
142C ILE* 5.3 2.3 - - + +
169C MET* 4.9 5.4 - - - -
171C ILE* 3.1 29.2 - - + +
198C PHE* 4.5 9.6 - + - -
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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
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103C PHE* 2.9 49.8 + - + +
104C ALA* 3.2 10.7 + - - -
106C TYR* 1.3 79.4 - - + +
108C ALA* 1.3 59.0 + - - +
110C LEU 4.0 10.8 - - - +
111C GLU* 5.6 0.5 - - - +
139C LEU* 5.8 2.2 - - + -
140C TYR* 3.9 14.8 - - - +
255C ALA* 4.1 10.8 + - - +
259C GLY 6.0 0.7 - - - -
135D PHE* 5.9 2.5 - - + -
138D LYS* 5.7 8.9 - - - +
139D LEU* 5.8 7.9 - - + -
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Residues in contact with ALA 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 ALA 2.9 17.6 + - - +
105C VAL 3.9 3.4 - - - +
107C THR* 1.3 78.3 - - - +
109C LEU* 1.3 68.3 + - + +
110C LEU 5.1 0.2 - - - -
251C LYS* 3.7 35.8 + - + +
252C LEU* 4.0 18.2 - - + -
255C ALA* 3.4 20.2 - - + -
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Residues in contact with LEU 109 (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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105C VAL* 3.2 22.8 + - + +
108C ALA* 1.3 90.4 - - + +
110C LEU* 1.3 66.9 + - - +
114C ASP* 4.8 0.2 - - - +
169C MET* 3.5 30.1 - - + -
196C TYR* 4.0 47.8 + - + +
198C PHE* 5.7 1.1 - - + -
222C VAL* 4.0 19.1 - - + -
248C LEU* 3.4 30.1 - - + -
251C LYS* 5.4 3.6 - - + +
252C LEU* 5.2 1.8 - - + -
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Residues in contact with LEU 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 TYR* 2.8 35.8 + - + +
107C THR* 4.0 12.1 - - - +
108C ALA 5.1 0.2 - - - -
109C LEU* 1.3 85.3 - - + +
111C GLU* 1.3 71.6 + - - +
112C PRO* 4.4 1.9 - - - +
114C ASP* 3.4 11.0 - - + +
116C VAL* 3.5 31.6 - - + -
140C TYR* 4.0 15.8 + - + -
168C LYS* 3.7 32.3 - - + +
169C MET* 4.0 33.2 - - + -
196C TYR* 4.9 2.0 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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