Contacts of the helix formed by residues 95 - 108 (chain A) in PDB entry 4DQ6
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 GLY 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A SER* 2.7 25.0 + - - -
94A PRO* 1.3 83.2 - - - +
96A VAL* 1.3 67.3 + - - +
97A ILE 3.4 2.0 - - - -
98A PRO* 3.4 13.4 - - - +
99A ALA* 3.3 5.9 + - - +
245A SER* 3.2 13.4 + - - -
401A PLP 3.5 13.0 - - - -
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Residues in contact with VAL 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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95A GLY* 1.3 72.5 - - - -
97A ILE* 1.3 65.8 + - + +
99A ALA* 3.2 7.9 + - - +
100A ILE* 3.0 35.3 + - + +
200A ASP* 3.6 30.3 - - - +
202A ILE* 3.9 26.7 - - + -
230A CYS* 3.8 22.7 - - + -
231A MET 4.5 4.5 - - - +
245A SER* 4.3 13.7 - - - -
401A PLP 2.9 27.2 + - + +
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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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96A VAL* 1.3 82.3 - - + +
98A PRO* 1.3 66.6 - - - +
100A ILE* 3.2 20.1 + - + -
101A SER* 2.8 22.7 + - - -
121A TYR* 3.9 21.8 - - + +
123A PRO* 3.8 32.5 - - + +
124A PHE* 4.5 9.4 - - + -
127A VAL* 4.0 25.1 - - + -
401A PLP 3.0 12.6 + - + +
264B ARG 5.3 0.4 - - - +
265B ILE 5.3 0.2 - - - -
266B ASP* 3.5 32.5 - - + +
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Residues in contact with PRO 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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93A SER* 3.9 6.7 - - - +
94A PRO* 4.7 3.4 - - + -
95A GLY* 3.4 25.8 - - - +
97A ILE* 1.3 95.0 - - + +
99A ALA* 1.3 61.8 + - - +
101A SER* 3.3 3.0 + - - -
102A LEU* 3.0 29.2 + - + +
262A PHE* 4.8 4.9 - - + -
401A PLP 3.6 5.4 - - - +
265B ILE* 3.1 31.7 - - + +
266B ASP* 3.7 15.0 - - - +
267B ILE* 3.8 18.6 - - + -
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Residues in contact with ALA 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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93A SER* 3.6 15.1 + - - +
95A GLY 3.3 4.2 + - - +
96A VAL* 3.2 10.1 + - - +
98A PRO* 1.3 77.7 - - - +
100A ILE* 1.3 60.1 + - - +
102A LEU* 3.2 3.3 + - - +
103A LEU* 2.9 34.1 + - + +
230A CYS* 4.4 7.6 - - - -
247A VAL* 3.5 32.3 - - + -
258A LEU* 4.2 2.9 - - + +
262A PHE* 4.2 11.9 - - + -
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Residues in contact with ILE 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 VAL* 3.0 33.6 + - + +
97A ILE* 3.7 15.9 - - + +
99A ALA* 1.3 74.5 - - - +
101A SER* 1.3 57.9 + - - +
103A LEU* 3.3 8.1 + - - +
104A ILE* 2.9 47.8 + - + +
124A PHE* 4.7 2.5 - - + -
127A VAL* 4.1 9.6 - - + -
166A ILE* 4.1 28.7 - - + -
198A ILE* 4.0 23.3 - - + -
200A ASP* 4.4 10.3 - - + +
230A CYS* 4.0 15.0 - - - -
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Residues in contact with SER 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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97A ILE 2.8 17.4 + - - -
98A PRO 3.5 5.2 - - - -
99A ALA 3.2 0.2 - - - -
100A ILE* 1.3 77.5 - - - +
102A LEU* 1.3 61.8 + - - +
104A ILE* 3.3 4.5 + - - +
105A ASN* 3.1 22.0 + - - +
127A VAL* 3.6 14.6 - - - +
131A ASN* 3.1 19.0 + - - +
264B ARG* 2.7 33.8 + - - +
265B ILE* 3.8 12.9 - - - +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PRO 3.0 16.6 + - - +
99A ALA 3.8 0.2 - - - +
101A SER* 1.3 75.9 - - - +
103A LEU* 1.3 64.2 + - - +
105A ASN* 3.3 6.2 + - + +
106A GLU* 3.0 28.8 + - - +
258A LEU* 3.8 13.0 - - + -
261A ALA* 3.9 19.5 - - + -
262A PHE* 3.5 43.1 - - + -
264A ARG* 3.8 26.5 - - - +
265A ILE* 3.8 23.3 - - + -
264B ARG* 5.6 1.6 - - - +
265B ILE* 4.2 18.2 - - + -
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Residues in contact with LEU 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 ALA 2.9 26.1 + - - +
100A ILE* 3.6 7.2 - - - +
102A LEU* 1.3 75.4 - - - +
104A ILE* 1.3 56.7 + - - +
106A GLU* 4.8 3.8 - - + -
107A LEU* 2.8 53.9 + - + +
164A LEU* 4.9 0.4 - - - -
198A ILE* 3.9 28.7 - - + -
228A ILE* 3.7 33.9 - - + -
230A CYS* 4.8 2.9 - - - -
247A VAL* 4.5 9.6 - - + -
249A LEU* 4.2 4.5 - - + -
254A ASP* 5.2 2.5 - - + +
257A LEU* 6.2 1.3 - - + -
258A LEU* 3.9 30.7 - - + +
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Residues in contact with ILE 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 ILE* 2.9 28.0 + - + +
101A SER 3.6 4.5 - - - +
103A LEU* 1.3 76.3 - - - +
105A ASN* 1.3 62.7 + - - +
108A THR* 2.5 35.3 + - - +
114A ILE* 3.6 26.2 - - + -
127A VAL* 3.8 37.5 - - + +
128A VAL* 4.1 16.6 - - + -
131A ASN* 3.9 23.6 - - + +
133A ARG* 3.6 7.3 + - + +
164A LEU* 4.2 13.5 - - + -
166A ILE* 4.2 5.4 - - + -
198A ILE* 5.0 2.0 - - + -
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Residues in contact with ASN 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 SER 3.1 10.5 + - - +
102A LEU* 3.6 10.8 - - + +
104A ILE* 1.3 80.4 - - - +
106A GLU* 1.3 79.6 + - - +
108A THR 3.0 17.3 - - - +
131A ASN* 4.2 12.0 + - - +
133A ARG* 3.2 24.7 + - - +
264A ARG* 3.6 14.9 - - - +
264B ARG* 5.8 6.1 - - - +
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Residues in contact with GLU 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 LEU 3.0 19.3 + - - +
103A LEU* 4.1 4.7 - - + +
105A ASN* 1.3 89.8 + - - +
107A LEU* 1.3 61.1 + - + +
108A THR 3.4 1.9 + - - +
257A LEU* 3.9 49.5 - - + +
258A LEU* 5.3 0.9 - - - -
261A ALA* 3.7 22.2 - - + -
264A ARG* 2.9 30.6 + - - -
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Residues in contact with LEU 107 (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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103A LEU* 2.8 38.0 + - + +
106A GLU* 1.3 76.2 - - + +
108A THR* 1.3 62.4 + - - +
163A LYS* 5.2 2.8 - - - +
164A LEU* 4.1 32.0 - - + +
196A LYS* 5.1 5.4 - - + -
198A ILE* 4.7 2.9 - - + -
228A ILE* 3.9 25.1 - - + -
254A ASP* 3.8 19.1 - - + +
257A LEU* 3.7 24.2 - - + -
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Residues in contact with THR 108 (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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104A ILE* 2.5 21.3 + - - +
105A ASN 3.0 8.7 - - - +
106A GLU 3.4 1.8 - - - +
107A LEU* 1.3 82.4 - - - +
109A LYS* 1.3 56.5 + - - +
112A ASP* 3.5 19.5 - - + -
114A ILE* 4.5 5.6 - - + -
133A ARG* 2.7 38.9 + - - +
163A LYS* 3.8 24.2 - - + -
164A LEU* 3.7 26.2 - - + -
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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