Contacts of the helix formed by residues 3 - 17 (chain A) in PDB entry 1Y88
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 ASN 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 1.3 66.4 + - - +
5A TYR* 2.9 18.6 - - - +
6A PHE* 3.4 18.2 + - + +
7A GLN* 2.9 48.2 + - - +
137A LYS* 3.3 38.9 - - + +
140A LEU* 6.0 2.2 - - + -
141A ASP* 5.3 0.4 - - - -
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Residues in contact with LEU 4 (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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3A ASN* 1.3 83.6 - - - +
5A TYR* 1.3 61.6 + - - +
7A GLN* 3.4 20.4 - - - +
8A GLY* 3.1 21.0 + - - -
36A GLU* 5.7 4.9 - - + +
38A ASP* 3.4 39.5 - - - +
52A CYS* 3.7 20.0 - - + +
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Residues in contact with TYR 5 (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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3A ASN* 2.9 10.7 - - - +
4A LEU* 1.3 76.4 - - - +
6A PHE* 1.3 64.2 + - - +
8A GLY* 4.1 0.2 - - - -
9A HIS* 2.8 57.8 + + - -
25A ASN* 5.0 22.9 - - + -
141A ASP* 4.4 15.0 - - + +
144A VAL* 3.5 27.8 - - + -
145A ARG* 3.6 42.4 + - + +
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Residues in contact with PHE 6 (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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3A ASN* 3.4 18.8 + - + +
5A TYR* 1.3 78.1 - - - +
7A GLN* 1.3 68.4 + - + +
9A HIS* 3.2 3.6 + - - +
10A MET* 2.8 56.3 + - + -
54A PHE* 6.3 0.4 - + - -
129A PRO* 3.8 17.5 - - + -
130A ILE* 3.9 12.8 - - + -
131A THR* 3.8 27.1 - - + -
140A LEU* 4.2 14.1 - - + -
141A ASP* 5.4 1.7 + - - +
144A VAL* 3.5 31.0 - - + -
149A VAL* 3.6 35.0 - - + -
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Residues in contact with GLN 7 (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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3A ASN* 2.9 37.3 + - - +
4A LEU* 3.4 26.3 - - - +
6A PHE* 1.3 85.0 - - + +
8A GLY* 1.3 58.5 + - - +
10A MET* 3.3 4.0 + - - +
11A VAL* 2.9 34.3 + - - +
52A CYS* 4.0 8.9 - - + +
54A PHE* 3.3 63.1 + - + +
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Residues in contact with GLY 8 (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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4A LEU 3.1 16.2 + - - -
5A TYR 4.1 0.4 - - - -
7A GLN* 1.3 76.0 - - - +
9A HIS* 1.3 58.3 + - - +
11A VAL 3.5 0.3 + - - -
12A ALA* 2.9 26.5 + - - +
24A THR* 4.0 8.1 - - - -
38A ASP* 4.5 8.3 - - - -
39A VAL* 3.4 23.6 - - - +
52A CYS* 4.2 8.7 - - - -
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Residues in contact with HIS 9 (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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5A TYR* 2.8 67.1 + + - +
6A PHE 3.2 4.4 + - - +
8A GLY* 1.3 73.7 - - - +
10A MET* 1.3 64.3 + - - +
12A ALA* 3.4 2.4 + - - +
13A ARG* 3.0 24.8 + - - +
24A THR* 3.5 35.3 + - + -
25A ASN* 5.8 0.4 - - + -
144A VAL* 3.6 23.1 + - + +
145A ARG* 5.4 1.4 + - - -
147A GLY* 5.1 7.2 - - - -
149A VAL* 3.8 19.6 - - + +
309A SO4 5.4 4.5 + - - -
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Residues in contact with MET 10 (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 PHE* 2.8 48.1 + - + +
7A GLN* 3.7 2.5 - - - +
9A HIS* 1.3 72.5 - - - +
11A VAL* 1.3 66.6 + - + +
13A ARG* 3.2 3.8 + - - +
14A LEU* 3.0 35.2 + - + +
54A PHE* 4.0 32.3 - - + -
110A TRP* 5.8 1.8 - - + -
118A ILE* 4.2 22.9 - - + -
122A LEU* 4.3 9.2 - - + -
129A PRO* 4.0 23.1 - - - -
149A VAL* 4.4 10.7 - - + +
150A PHE* 4.0 18.6 - - + -
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Residues in contact with VAL 11 (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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7A GLN 2.9 20.9 + - - +
8A GLY 3.9 3.1 - - - +
10A MET* 1.3 81.1 - - + +
12A ALA* 1.3 62.7 + - - +
14A LEU* 3.3 10.7 + - + +
15A LEU* 3.0 29.6 + - + +
39A VAL* 4.2 11.7 - - + -
50A ILE* 4.3 3.4 - - + -
52A CYS* 3.9 17.3 - - - -
54A PHE* 4.3 12.3 - - + -
87A PHE* 3.9 52.7 - - + -
118A ILE* 5.2 1.1 - - + -
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Residues in contact with ALA 12 (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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8A GLY 2.9 21.8 + - - +
9A HIS* 3.8 4.0 - - - +
11A VAL* 1.3 72.0 - - - +
13A ARG* 1.3 58.3 + - - +
15A LEU* 3.1 2.0 + - - -
16A GLU* 2.8 35.8 + - - +
22A THR* 3.5 30.9 - - - +
24A THR* 3.7 20.6 - - + -
39A VAL* 4.1 8.7 - - + +
309A SO4 5.6 0.2 - - - +
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Residues in contact with ARG 13 (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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9A HIS 3.0 17.8 + - - +
10A MET 3.5 4.3 - - - +
12A ALA* 1.3 78.1 - - - +
14A LEU* 1.3 61.3 + - - +
16A GLU* 3.2 21.6 + - - +
17A GLU* 3.0 39.3 + - - +
147A GLY 3.8 9.9 + - - -
149A VAL* 3.6 18.3 - - + +
150A PHE* 3.3 27.6 - - + -
152A ARG* 4.6 8.9 - - - +
153A ASP* 2.7 44.8 + - - -
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Residues in contact with LEU 14 (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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10A MET* 3.0 29.2 + - + +
11A VAL* 3.7 11.9 - - + +
13A ARG* 1.3 75.2 - - - +
15A LEU* 1.3 63.1 + - + +
17A GLU* 3.3 22.9 + - - +
18A HIS* 3.0 26.8 + - + +
87A PHE* 5.6 2.0 - - + -
118A ILE* 4.3 20.9 - - + -
121A LEU* 3.9 47.1 - - + +
122A LEU* 4.0 16.4 - - + -
127A LEU* 3.8 18.2 - - + -
150A PHE* 4.0 6.3 - - + -
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Residues in contact with LEU 15 (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 VAL* 3.0 27.2 + - + +
12A ALA 3.7 5.6 - - - +
14A LEU* 1.3 76.6 - - + +
16A GLU* 1.3 62.0 + - - +
18A HIS* 2.8 19.8 + - + +
19A GLY 3.2 0.5 + - - -
20A PHE* 3.1 44.6 + - + -
22A THR* 4.2 3.1 - - + -
39A VAL* 4.8 4.0 - - + -
41A ALA* 3.9 11.7 - - + -
50A ILE* 3.3 34.5 - - + -
85A TRP* 3.7 26.5 - - + -
87A PHE* 4.1 13.7 - - + -
121A LEU* 5.6 4.7 - - + -
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Residues in contact with GLU 16 (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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12A ALA* 2.8 15.2 + - - +
13A ARG* 3.5 31.9 + - - +
15A LEU* 1.3 76.0 - - - +
17A GLU* 1.3 61.0 + - + +
18A HIS 3.2 0.5 + - - -
19A GLY* 3.2 12.0 + - - -
20A PHE 3.4 20.4 + - - +
21A GLU* 5.2 0.4 - - - -
22A THR* 3.1 29.5 + - + +
309A SO4 5.7 0.5 + - - -
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Residues in contact with GLU 17 (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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13A ARG* 3.0 32.2 + - + +
14A LEU* 3.5 21.4 - - - +
15A LEU 3.1 0.4 - - - -
16A GLU* 1.3 76.2 - - + +
18A HIS* 1.3 68.4 + - - +
19A GLY 3.4 1.7 + - - -
121A LEU 4.6 0.5 - - - +
125A LYS* 4.2 36.6 + - - +
127A LEU* 3.3 39.8 - - - +
150A PHE* 4.1 7.1 - - - -
152A ARG* 5.5 1.0 + - - -
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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