Contacts of the helix formed by residues 98 - 110 (chain A) in PDB entry 1A4Y
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR* 1.3 74.7 - - - +
99A ALA* 1.3 60.8 + - - +
101A CYS* 3.1 20.6 + - - +
123A LEU 3.5 9.3 + - - -
124A LEU* 3.4 21.7 + - - -
127A ALA* 5.7 1.8 - - - -
128A GLY* 3.6 16.7 - - - -
131A LEU* 4.0 7.6 - - - +
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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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69A ASP* 3.8 16.6 - - + +
97A THR* 2.9 4.2 + - - +
98A GLY* 1.3 76.9 - - - +
100A GLY* 1.3 60.2 + - - +
101A CYS 3.1 1.2 + - - -
102A GLY* 3.8 8.9 + - - -
103A VAL* 4.9 3.3 - - - +
131A LEU* 5.1 3.2 - - - +
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Residues in contact with GLY 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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69A ASP* 3.1 27.7 + - - -
72A VAL* 5.4 0.7 - - - +
96A LEU* 3.8 14.6 - - - +
97A THR 2.7 16.4 + - - -
99A ALA* 1.3 70.1 - - - +
101A CYS* 1.3 57.6 + - - -
102A GLY 3.2 5.5 + - - -
103A VAL* 3.5 21.9 - - - +
104A LEU* 3.5 14.3 + - - +
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Residues in contact with CYS 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 THR 4.1 2.7 - - - -
98A GLY 3.1 15.2 + - - +
100A GLY* 1.3 76.4 - - - +
102A GLY* 1.3 59.7 + - - +
104A LEU* 3.7 17.0 - - - +
105A SER* 2.9 27.7 + - - -
124A LEU* 3.9 31.4 - - - -
128A GLY* 3.3 36.6 - - - +
131A LEU* 3.8 9.1 - - + +
132A LEU* 4.3 12.9 + - + +
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Residues in contact with GLY 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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99A ALA 3.8 5.9 + - - -
100A GLY 3.2 1.6 - - - -
101A CYS* 1.3 75.8 - - - +
103A VAL* 1.3 66.8 + - - +
105A SER* 2.9 13.9 + - - -
106A SER* 3.1 16.4 + - - -
131A LEU* 3.5 27.1 - - - +
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Residues in contact with VAL 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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69A ASP 4.7 2.9 - - - +
72A VAL* 5.6 2.0 - - + -
73A HIS* 3.0 58.8 - - + +
76A LEU* 4.2 16.4 - - + -
80A GLN* 4.6 5.6 - - - +
99A ALA 4.9 2.5 - - - +
100A GLY* 3.5 22.0 - - - +
102A GLY* 1.3 72.0 - - - +
104A LEU* 1.3 62.8 + - - +
106A SER* 3.2 9.3 + - - -
107A THR* 3.0 27.6 + - - +
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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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72A VAL* 5.1 2.7 - - + -
76A LEU* 3.9 22.4 - - + -
89A LEU* 5.0 3.4 - - + -
91A LEU* 4.1 19.1 - - + -
96A LEU* 4.4 16.6 - - + -
100A GLY 3.5 14.7 + - - +
101A CYS* 3.7 13.7 - - - +
103A VAL* 1.3 81.0 - - - +
105A SER* 1.3 63.0 + - - +
107A THR* 3.4 3.4 + - + -
108A LEU* 3.0 29.4 + - + +
117A LEU* 4.7 14.4 - - + -
119A LEU* 4.0 32.1 - - + -
124A LEU* 5.6 1.3 - - + -
132A LEU* 3.6 17.5 - - + -
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Residues in contact with SER 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 CYS 2.9 20.0 + - - -
102A GLY 2.9 5.8 + - - -
104A LEU* 1.3 78.0 - - - +
106A SER* 1.3 60.2 + - - +
108A LEU* 3.6 5.9 + - - +
109A ARG* 2.8 36.3 + - - +
131A LEU* 2.8 32.2 + - - -
132A LEU* 3.6 3.4 + - - +
134A GLU* 3.9 2.1 - - - +
135A GLY* 2.9 26.8 + - - -
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Residues in contact with SER 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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80A GLN* 4.0 10.1 - - - -
102A GLY 3.1 14.4 + - - -
103A VAL* 3.2 9.8 + - - -
105A SER* 1.3 71.6 - - - +
107A THR* 1.3 69.9 - - - +
109A ARG* 2.8 25.6 + - - +
110A THR* 3.1 16.2 + - - +
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Residues in contact with THR 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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76A LEU* 3.3 38.6 - - + +
79A LEU* 5.2 2.9 - - + -
80A GLN* 3.2 21.5 + - - +
89A LEU* 5.6 4.5 - - + -
103A VAL* 3.0 11.9 + - - +
104A LEU* 3.6 8.7 - - + -
106A SER* 1.3 76.8 - - - +
108A LEU* 1.3 66.1 + - + +
110A THR* 2.7 16.7 + - - -
111A LEU* 3.1 40.4 + - + +
114A LEU* 5.4 6.7 - - + -
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Residues in contact with LEU 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 LEU* 3.0 20.4 + - + +
105A SER* 3.7 6.5 - - - +
107A THR* 1.3 81.0 - - + +
109A ARG* 1.3 61.6 + - - +
110A THR 3.3 0.5 + - - -
111A LEU* 3.6 12.2 + - - +
114A LEU* 3.6 31.0 - - + -
117A LEU* 3.8 19.3 - - + -
132A LEU* 4.1 26.0 - - + +
135A GLY 4.4 4.3 - - - -
136A LEU* 3.4 33.9 - - + +
140A GLN 4.4 0.2 - - - +
141A CYS* 3.8 36.0 - - - +
143A LEU* 4.7 4.7 - - + -
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Residues in contact with ARG 109 (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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105A SER* 2.8 29.7 + - - +
106A SER* 2.8 15.9 + - - +
108A LEU* 1.3 75.9 - - - +
110A THR* 1.3 62.8 + - + +
111A LEU 3.6 0.2 - - - -
134A GLU* 3.4 51.9 + - - +
135A GLY* 3.6 11.2 - - - +
138A ASP* 2.8 37.5 + - + +
140A GLN* 3.2 29.6 - - - +
141A CYS 4.9 0.4 - - - +
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Residues in contact with THR 110 (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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80A GLN* 3.5 30.0 - - + +
106A SER* 3.3 17.1 + - - +
107A THR* 2.7 15.7 + - - -
109A ARG* 1.3 79.3 - - + +
111A LEU* 1.3 62.8 + - - +
112A PRO* 3.7 10.2 - - - +
140A GLN* 5.1 1.6 - - - -
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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