Contacts of the helix formed by residues 93 - 109 (chain A) in PDB entry 1DIN
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 MET 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TRP* 4.6 8.3 - - + +
91A PHE* 3.0 49.2 + - + +
92A ASP* 1.3 73.2 + - - +
94A GLU* 1.3 74.8 + - - +
96A GLY* 3.0 1.9 + - - -
97A VAL* 3.0 27.8 + - - +
124A LEU* 3.3 24.7 - - + -
127A ALA* 5.2 10.1 - - - -
128A LEU* 4.0 15.8 - - - +
131A LEU* 4.7 15.3 - - + -
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Residues in contact with GLU 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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11A TYR* 4.8 2.0 + - - -
92A ASP* 3.0 9.6 + - - +
93A MET* 1.3 89.1 - - - +
95A ALA* 1.3 64.2 - - - +
97A VAL* 3.3 10.4 + - + +
98A GLY* 3.2 16.6 + - - -
131A LEU* 5.3 4.9 - - - +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.4 25.9 - - - +
66A ARG* 3.8 25.1 - - - +
92A ASP* 3.0 31.4 + - + +
94A GLU* 1.3 76.7 - - - +
96A GLY* 1.3 60.0 + - - +
98A GLY* 3.2 1.2 + - - -
99A ASP* 2.9 34.7 + - - +
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.3 4.2 - - - +
91A PHE* 3.9 21.5 - - - -
92A ASP 2.8 15.3 + - - -
93A MET 3.0 4.9 + - - -
95A ALA* 1.3 78.1 - - - +
97A VAL* 1.3 55.6 + - - +
99A ASP* 3.4 9.2 + - - +
100A LEU* 2.9 32.8 + - - +
128A LEU* 4.3 7.4 - - - -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A MET 3.0 16.8 + - - +
94A GLU* 3.7 10.5 - - + +
95A ALA 3.3 0.2 - - - -
96A GLY* 1.3 75.6 - - - +
98A GLY* 1.3 58.7 + - - +
100A LEU* 3.1 7.7 + - - +
101A GLU* 2.9 27.9 + - - +
128A LEU* 3.9 9.0 - - + -
131A LEU* 3.7 36.6 - - + -
132A VAL* 4.3 12.6 - - + -
135A LYS* 4.3 19.7 - - + -
137A TYR* 3.9 23.6 - - + +
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.7 11.2 + - - -
11A TYR* 3.7 21.2 + - - +
94A GLU 3.2 8.7 + - - -
95A ALA 3.2 6.5 + - - -
97A VAL* 1.3 76.7 - - - +
99A ASP* 1.3 61.3 + - - +
101A GLU* 3.2 15.9 + - - +
102A ALA* 3.2 17.7 + - - +
105A ARG* 5.2 0.7 + - - -
137A TYR* 5.8 0.4 - - - -
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 2.7 25.0 + - - -
14A HIS* 3.8 8.4 + - - -
16A PHE* 3.3 29.7 - - + -
62A ASP 5.3 0.5 - - - +
63A LEU* 3.9 27.3 - - + +
66A ARG* 2.8 38.1 + - - +
95A ALA 2.9 18.2 + - - +
96A GLY* 3.8 5.5 - - - +
98A GLY* 1.3 74.7 - - - +
100A LEU* 1.3 63.7 + - - +
102A ALA* 3.2 2.1 + - - -
103A ALA* 3.1 17.3 + - - +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 4.0 18.4 - - + -
34A ALA* 4.3 12.8 - - + -
61A PRO* 3.9 25.4 - - + -
63A LEU* 4.2 13.5 - - + -
96A GLY 2.9 20.3 + - - +
97A VAL 3.1 4.9 + - - +
99A ASP* 1.3 75.9 - - - +
101A GLU* 1.4 65.6 + - - +
103A ALA* 3.1 3.4 + - - +
104A ILE* 2.8 33.5 + - + +
119A LEU* 4.2 9.6 - - + -
128A LEU* 3.7 36.8 - - + +
132A VAL* 3.9 22.2 - - + -
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 5.5 5.2 - - - +
97A VAL 2.9 8.7 + - - +
98A GLY* 3.2 15.8 + - - +
100A LEU* 1.4 76.1 - - - +
102A ALA* 1.3 62.1 + - - +
104A ILE* 3.2 6.6 + - - +
105A ARG* 2.8 62.7 + - + +
137A TYR* 3.4 58.9 + - + -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.7 12.4 - - + +
9A GLN 3.6 23.6 - - - +
10A SER* 4.0 11.9 - - - +
11A TYR 5.1 0.2 - - - +
16A PHE* 4.2 2.5 - - + -
98A GLY 3.2 10.7 + - - +
99A ASP 3.4 10.1 - - - +
101A GLU* 1.3 78.1 - - - +
103A ALA* 1.3 56.5 + - - +
105A ARG* 3.5 19.7 + - - +
106A TYR* 3.0 27.0 + - - +
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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
----------------------------------------------------------
8A ILE* 4.3 10.3 - - + +
16A PHE* 4.4 4.7 - - + -
32A VAL* 4.2 13.5 - - + +
59A VAL* 4.9 4.9 - - + +
61A PRO* 4.1 30.3 - - + -
99A ASP 3.1 12.9 + - - +
100A LEU 3.1 7.6 + - - +
102A ALA* 1.3 73.5 - - - +
104A ILE* 1.3 60.7 + - - +
106A TYR* 3.3 10.8 + - - +
107A ALA* 2.9 28.2 + - - +
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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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32A VAL* 4.0 24.2 - - + -
100A LEU* 2.8 26.0 + - + +
101A GLU* 3.5 6.1 - - - +
103A ALA* 1.3 73.8 - - - +
105A ARG* 1.3 65.1 + - + +
107A ALA* 3.0 3.7 + - - +
108A ARG* 2.9 33.0 + - - +
117A VAL* 3.9 15.0 - - + +
119A LEU* 4.7 7.4 - - + -
132A VAL* 4.0 18.8 - - + -
137A TYR* 3.6 28.9 - - + +
138A VAL* 3.3 26.9 - - + -
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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
----------------------------------------------------------
9A GLN 5.4 1.4 + - - -
10A SER 5.8 0.2 - - - -
11A TYR* 5.3 11.9 - - - +
98A GLY 5.2 0.8 + - - -
101A GLU* 2.8 61.0 + - + +
102A ALA* 3.8 23.4 - - - +
104A ILE* 1.3 76.1 - - + +
106A TYR* 1.3 65.4 + - - +
108A ARG* 3.1 15.3 + - - +
109A HIS* 2.9 32.6 - - + +
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Residues in contact with TYR 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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6A ILE* 3.7 35.2 - - + +
7A SER 5.1 5.4 - - - -
8A ILE* 3.9 34.3 - - + -
20A VAL* 4.6 6.5 - - + +
59A VAL* 4.4 21.1 - - + -
102A ALA 3.0 15.5 + - - +
103A ALA* 3.3 13.5 - - - +
105A ARG* 1.3 79.0 - - - +
107A ALA* 1.3 64.6 + - - +
109A HIS* 3.4 7.1 + - - +
110A GLN* 2.8 60.8 + - + +
112A TYR* 4.5 3.6 + - - -
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Residues in contact with ALA 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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30A VAL* 3.6 35.7 - - + +
32A VAL* 4.1 11.4 - - + -
59A VAL* 4.8 2.9 - - + -
103A ALA 2.9 13.8 + - - +
104A ILE 3.3 9.4 - - - +
106A TYR* 1.3 82.7 - - - +
108A ARG* 1.3 64.6 + - - +
109A HIS 3.2 1.0 + - - -
110A GLN* 3.5 7.9 + - - +
113A SER* 3.4 18.5 + - - -
117A VAL* 4.1 9.0 - - + -
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 2.9 17.5 + - - +
105A ARG* 3.1 15.2 + - - +
107A ALA* 1.3 78.9 - - - +
109A HIS* 1.3 76.9 + - + +
110A GLN 3.7 0.6 - - - +
113A SER* 3.4 16.9 + - - +
115A GLY* 2.8 44.6 + - - +
117A VAL* 3.6 21.8 - - + +
137A TYR 3.1 25.1 + - - -
138A VAL* 3.8 8.7 - - - +
139A ASP* 2.9 33.7 + - - +
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Residues in contact with HIS 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 ARG* 2.9 34.4 + - + +
106A TYR* 3.4 6.9 + - - +
107A ALA 3.2 0.8 - - - -
108A ARG* 1.3 93.2 + - + +
110A GLN* 1.3 71.0 + - - +
111A PRO* 3.7 3.3 - - - +
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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
------------------------------------------------------------
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