Contacts of the helix formed by residues 93 - 105 (chain A) in PDB entry 1JSC
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 THR 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLY 5.4 0.2 - - - +
92A LEU* 1.3 73.5 - - - +
94A GLY* 1.3 67.2 + - - +
95A GLY* 3.8 4.7 + - - -
96A GLN* 2.6 42.8 + - - +
97A ILE* 2.9 24.7 + - - +
254A THR 4.2 4.5 - - - -
255A ALA* 4.2 9.6 - - - +
256A ALA 3.1 8.7 - - - +
257A ILE* 3.6 25.4 - - + -
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 1.3 70.9 - - - +
95A GLY* 1.3 52.3 + - - +
97A ILE* 3.2 3.9 + - - +
98A PHE* 2.7 36.3 + - - +
223A VAL* 4.0 12.7 - - - +
226A LEU* 3.5 22.8 - - - +
254A THR* 3.0 20.6 + - - -
256A ALA 3.0 11.7 + - - -
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 3.1 5.0 + - - -
94A GLY* 1.3 77.8 - - - +
96A GLN* 1.3 56.4 + - - +
98A PHE* 3.4 8.5 + - - +
99A ASN 3.0 20.4 + - - -
120A PRO* 3.8 22.2 - - - -
121A VAL* 4.3 8.1 - - - -
124A ALA* 3.3 19.6 - - - +
254A THR 3.1 10.4 + - - -
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLY 4.8 0.7 - - - +
92A LEU* 3.6 32.0 - - + +
93A THR* 2.6 45.7 + - - +
95A GLY* 1.3 74.4 - - - +
97A ILE* 1.3 61.6 + - - +
99A ASN* 3.2 9.5 - - - +
100A GLU* 2.8 29.1 + - - +
124A ALA* 4.7 5.4 - - + -
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 4.1 26.2 - - + +
92A LEU* 3.9 16.6 - - + -
93A THR 2.9 17.3 + - - +
94A GLY* 3.4 7.9 - - - +
96A GLN* 1.3 77.0 - - - +
98A PHE* 1.3 52.0 + - - +
100A GLU* 3.0 8.5 + - - +
101A MET* 2.7 40.3 + - + +
223A VAL* 3.8 29.6 - - + +
226A LEU* 4.3 7.2 - - + -
227A PRO* 3.7 30.1 - - + -
258A LEU* 4.0 23.3 - - + -
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY 2.7 21.3 + - - +
95A GLY* 3.4 7.0 - - - +
97A ILE* 1.3 73.1 - - - +
99A ASN* 1.3 64.7 + - - +
101A MET* 3.1 2.8 + - - +
102A MET* 2.9 60.2 + - + +
110A VAL* 5.8 2.5 - - + -
121A VAL* 3.4 35.4 - - + -
125A ILE* 3.7 19.3 - - + -
158A VAL* 5.1 1.8 - - + -
160A LEU* 4.6 6.7 - - + -
187A PHE* 3.6 48.5 - + + -
226A LEU* 4.7 7.0 - - + -
230A ILE* 3.9 22.7 - - + -
249A LEU* 4.4 8.5 - - + -
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLY 3.0 14.4 + - - +
96A GLN* 3.2 13.7 - - - +
98A PHE* 1.3 83.6 - - - +
100A GLU* 1.3 63.3 + - - +
102A MET 3.2 7.6 + - - -
103A SER* 3.3 3.6 + - - -
124A ALA* 3.0 34.3 + - + +
125A ILE* 3.9 4.3 - - + +
128A SER* 3.6 7.4 - - - -
130A LYS* 2.8 39.0 + - - -
131A PHE* 3.1 37.2 - - - -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.4 34.5 - - + -
92A LEU* 5.4 4.7 - - + -
96A GLN 2.8 16.2 + - - +
97A ILE* 3.0 8.9 + - - +
99A ASN* 1.3 73.9 + - - +
101A MET* 1.3 63.7 + - - +
103A SER* 3.2 10.0 + - - -
104A ARG* 3.1 39.5 + - - +
130A LYS* 4.4 12.9 + - - +
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Residues in contact with MET 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.9 28.9 - - - -
97A ILE* 2.7 27.9 + - + +
98A PHE 3.6 4.7 - - - +
100A GLU* 1.3 69.0 - - - +
102A MET* 1.3 68.4 + - - +
104A ARG* 3.1 15.6 + - + +
105A GLN* 3.0 27.7 + - - +
227A PRO* 4.0 19.7 - - + +
230A ILE* 3.7 33.9 - - + -
231A ASN* 3.3 41.7 - - - +
267A THR 3.8 10.1 - - - +
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Residues in contact with MET 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 2.9 54.9 + - + +
99A ASN 3.2 2.7 + - - +
101A MET* 1.3 77.0 - - - +
103A SER* 1.3 61.4 + - - +
105A GLN* 3.0 7.7 + - - -
107A VAL* 2.9 68.0 + - + +
110A VAL* 4.5 3.4 - - + -
125A ILE* 4.1 8.3 - - + -
131A PHE* 3.3 21.1 - - + -
158A VAL* 3.4 29.2 - - + -
187A PHE* 4.4 3.8 - - - -
230A ILE* 5.2 3.6 - - - -
234A PHE* 3.9 14.8 - - + -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASN 3.3 3.4 + - - -
100A GLU* 3.2 17.2 + - - -
101A MET 3.2 0.2 - - - -
102A MET* 1.3 79.1 - - - +
104A ARG* 1.3 57.5 + - - +
106A ASN* 2.9 25.9 + - - +
107A VAL 4.6 5.8 - - - +
130A LYS* 3.0 33.4 + - - +
131A PHE* 3.8 6.9 - - - -
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP* 5.2 1.0 + - - -
88A SER* 3.9 12.9 + - - -
89A PHE* 3.4 31.7 - - - -
100A GLU* 3.1 28.9 + - - +
101A MET* 3.1 18.1 + - + +
103A SER* 1.3 76.3 - - - +
105A GLN* 1.3 60.2 + - - +
106A ASN* 3.2 7.7 + - - +
267A THR* 2.8 56.3 + - - -
268A LEU* 4.2 11.0 - - - +
269A PRO* 3.6 27.6 - - + +
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Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A MET* 3.0 16.2 + - + +
102A MET* 3.6 8.1 - - - +
103A SER 3.0 0.6 - - - -
104A ARG* 1.3 76.8 - - + +
106A ASN* 1.3 71.8 + - - +
107A VAL* 3.2 15.5 + - + +
155A LYS* 5.2 0.5 + - - -
156A PRO* 5.7 3.3 - - - +
230A ILE* 4.6 4.0 - - + -
231A ASN* 2.7 41.4 + - - +
234A PHE* 3.4 47.0 - - + +
269A PRO* 3.7 20.8 - - - +
270A SER 4.9 1.2 - - - +
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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