Contacts of the helix formed by residues 95 - 106 (chain A) in PDB entry 1SFE
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 ALA 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A THR* 1.3 73.4 - - - +
96A PHE* 1.3 52.6 + - - +
98A GLN* 3.2 7.7 + - - +
99A GLN* 2.6 52.2 + - + +
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Residues in contact with PHE 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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94A THR* 3.6 7.8 + - - +
95A ALA* 1.3 76.3 - - - +
97A GLN* 1.3 57.6 + - + +
99A GLN* 3.1 13.6 + - - +
100A VAL* 2.7 50.2 + - + +
122A ILE* 4.0 18.8 - - + -
124A LYS* 4.1 27.8 - - + -
127A ALA* 4.5 6.7 - - + -
130A ALA* 3.5 39.7 - - + -
131A VAL* 3.8 25.8 - - + -
134A ALA* 4.4 4.3 - - + -
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Residues in contact with GLN 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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93A GLY* 3.4 9.2 - - - -
94A THR* 3.1 39.9 + - - +
96A PHE* 1.3 79.6 - - + +
98A GLN* 1.3 54.3 + - - +
100A VAL* 3.0 2.8 + - - +
101A TRP* 2.7 71.6 + - + -
133A SER 5.4 0.2 + - - -
134A ALA* 4.1 21.9 - - + +
137A ALA* 3.9 20.4 - - - +
139A LYS* 5.5 0.9 + - - -
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Residues in contact with GLN 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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91A ILE* 3.7 34.1 + - - +
92A ARG* 4.8 0.2 - - - +
93A GLY* 3.6 23.5 + - - +
94A THR 2.8 28.9 + - - +
95A ALA* 3.4 7.2 - - - +
97A GLN* 1.3 67.8 - - - +
99A GLN* 1.4 60.8 + - + +
101A TRP* 4.0 9.8 - - + +
102A GLN* 2.8 33.7 + - - +
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Residues in contact with GLN 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 ALA* 2.6 42.7 + - - +
96A PHE* 3.1 11.7 + - - +
98A GLN* 1.4 74.2 - - - +
100A VAL* 1.4 62.2 + - - +
102A GLN* 3.5 4.9 + - - +
103A ALA* 3.1 23.0 + - - +
122A ILE* 4.4 24.1 - - + +
124A LYS* 4.6 18.8 + - - +
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Residues in contact with VAL 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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96A PHE* 2.7 42.2 + - + +
97A GLN 3.0 5.4 + - - +
99A GLN* 1.4 74.3 - - - +
101A TRP* 1.3 59.6 + - + +
103A ALA* 3.2 6.6 + - - +
104A LEU* 3.0 30.0 + - + +
118A LEU* 3.7 25.6 - - + +
122A ILE* 4.2 15.3 - - + -
131A VAL* 4.4 6.1 - - + +
134A ALA* 3.6 25.1 - - + -
135A CYS* 3.9 18.2 - - - -
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Residues in contact with TRP 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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91A ILE* 3.7 24.9 - - + -
92A ARG 3.4 32.5 - - - -
93A GLY* 4.0 1.8 - - - -
97A GLN* 2.7 62.7 + - + +
98A GLN* 4.0 5.6 - - + +
100A VAL* 1.3 71.5 - - + +
102A GLN* 1.3 69.5 + - - +
104A LEU* 3.2 25.6 + - + +
105A ARG* 3.1 27.0 + - - +
134A ALA* 3.1 23.4 + - - +
137A ALA 3.5 23.6 - - - -
138A ASN* 3.8 18.0 - - + +
139A LYS* 4.3 7.6 - - + -
144A ILE* 3.9 25.9 - - + +
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Residues in contact with GLN 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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91A ILE* 5.9 0.5 - - - +
98A GLN 2.8 22.2 + - - +
99A GLN* 4.0 5.2 - - - +
101A TRP* 1.3 77.1 - - - +
103A ALA* 1.4 60.7 + - - +
105A ARG* 3.1 40.1 + - - +
106A THR* 3.6 19.6 + - + +
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Residues in contact with ALA 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 GLN 3.1 17.6 + - - +
100A VAL 3.2 3.8 + - - +
102A GLN* 1.4 73.8 - - - +
104A LEU* 1.4 63.5 + - - +
106A THR* 2.9 26.7 + - - +
107A ILE* 3.6 8.0 + - - +
118A LEU* 3.9 22.1 - - + +
121A ALA* 6.0 2.7 - - + -
122A ILE* 4.0 15.5 - - + -
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Residues in contact with LEU 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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100A VAL* 3.0 17.1 + - + +
101A TRP* 3.2 24.2 + - + +
103A ALA* 1.4 75.2 - - - +
105A ARG* 1.3 58.4 + - - +
106A THR 3.1 0.2 - - - -
107A ILE* 3.0 32.3 + - + +
118A LEU* 4.3 11.7 - - + -
135A CYS* 4.3 11.0 - - - -
144A ILE* 3.8 20.6 - - + -
145A PRO* 3.3 29.7 - - + +
146A CYS* 3.9 23.3 - - + -
149A VAL* 3.0 36.6 - - + -
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Residues in contact with ARG 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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85A LEU 5.3 6.3 + - - -
89A LEU* 3.8 20.1 - - - +
91A ILE* 3.7 24.5 - - - +
101A TRP 3.1 15.9 + - - +
102A GLN* 3.1 36.9 + - - +
104A LEU* 1.3 76.0 - - - +
106A THR* 1.3 59.8 + - - +
107A ILE 3.4 4.2 - - - +
143A VAL* 4.3 11.5 + - - +
144A ILE* 4.4 14.1 - - + -
145A PRO* 3.8 20.4 - - + +
148A ARG* 5.5 0.7 + - - -
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Residues in contact with THR 106 (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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102A GLN* 3.9 25.1 - - - +
103A ALA* 2.9 22.2 + - - +
104A LEU 3.1 0.4 - - - -
105A ARG* 1.3 77.2 - - - +
107A ILE* 1.3 64.8 + - - +
108A PRO* 3.2 9.2 - - - +
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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