Contacts of the helix formed by residues 2 - 16 (chain D) in PDB entry 1IB1
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 ASP 2 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D LYS* 1.3 65.6 + - - +
4D ASN* 3.2 20.4 + - - +
5D GLU* 3.0 55.6 + - + +
6D LEU* 3.1 37.5 + - - +
32D GLN* 4.6 6.2 - - - +
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Residues in contact with LYS 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP* 1.3 74.4 + - - +
4D ASN* 1.3 73.1 + - - +
6D LEU* 3.3 8.2 + - - +
7D VAL* 3.1 27.9 + - + +
29D VAL* 4.1 26.0 - - + +
32D GLN* 3.7 31.3 + - - +
34D ALA* 3.5 30.6 + - - +
35D GLU 4.6 5.5 + - - -
36D LEU* 5.8 0.4 - - - +
40D GLU* 3.7 28.0 + - - +
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Residues in contact with ASN 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP* 3.2 15.0 + - - +
3D LYS* 1.3 87.0 - - - +
5D GLU* 1.3 64.2 + - + +
7D VAL* 2.8 7.4 + - - +
8D GLN* 2.8 39.0 + - + +
40D GLU* 5.8 1.0 + - - -
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Residues in contact with GLU 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C GLN* 5.2 7.8 + - - -
78C MET* 4.5 16.6 - - + +
81C GLU* 4.9 8.1 - - - +
2D ASP* 3.0 42.3 + - - +
4D ASN* 1.3 73.6 - - + +
6D LEU* 1.3 58.8 + - + +
8D GLN* 3.3 8.6 + - - +
9D LYS* 2.7 36.1 + - - +
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Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP 3.1 25.8 + - - +
3D LYS 3.6 2.5 - - - +
4D ASN 3.1 0.6 - - - -
5D GLU* 1.3 80.8 - - + +
7D VAL* 1.3 57.9 + - - +
9D LYS* 3.5 7.4 + - + -
10D ALA* 2.9 29.6 + - - +
25D CYS* 3.4 26.4 - - - +
28D SER* 3.9 23.6 - - - -
29D VAL* 3.5 26.5 - - + +
32D GLN* 4.1 18.6 - - - +
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Residues in contact with VAL 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS* 3.1 17.9 + - + +
4D ASN* 2.8 9.2 + - - +
6D LEU* 1.3 73.4 - - - +
8D GLN* 1.3 67.1 + - - +
10D ALA* 3.1 6.5 + - - +
11D LYS* 2.9 39.7 + - + +
26D MET* 4.6 4.0 - - + -
29D VAL* 4.1 13.2 - - + -
39D GLU* 4.8 8.1 - - - +
40D GLU* 4.0 32.1 - - + +
43D LEU* 3.6 22.4 - - + -
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Residues in contact with GLN 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C MET* 4.1 14.5 - - + +
4D ASN* 2.8 42.2 + - + +
5D GLU* 3.5 8.7 - - - +
7D VAL* 1.3 82.8 - - - +
9D LYS* 1.3 62.3 + - - +
11D LYS* 3.3 34.1 + - - +
12D LEU* 3.0 21.5 + - - +
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Residues in contact with LYS 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C MET* 3.4 34.0 - - + -
82C TYR* 3.8 25.9 - - + +
85C LYS* 4.0 24.7 - - - +
5D GLU 2.7 21.8 + - - +
6D LEU* 3.9 9.2 - - + +
8D GLN* 1.3 72.9 - - - +
10D ALA* 1.3 57.1 + - - +
12D LEU* 3.2 3.4 - - - +
13D ALA* 2.8 27.9 + - - +
21D ASP* 5.0 7.5 - - - -
25D CYS* 3.6 22.7 - - - -
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Residues in contact with ALA 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU 2.9 19.7 + - - +
7D VAL* 3.1 5.8 + - - +
9D LYS* 1.3 74.1 - - - +
11D LYS* 1.3 65.0 + - - +
13D ALA 3.4 0.7 + - - +
14D GLU* 3.1 19.8 + - - +
22D MET* 3.3 27.9 - - + +
25D CYS* 3.8 14.6 - - + -
26D MET* 3.8 26.7 - - + -
43D LEU* 4.4 4.5 - - + -
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Residues in contact with LYS 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 2.9 30.0 + - + +
8D GLN* 3.6 25.5 - - - +
10D ALA* 1.3 76.5 - - - +
12D LEU* 1.3 61.3 + - - +
14D GLU* 3.6 13.2 + - - +
15D GLN* 3.4 33.7 + - - +
39D GLU* 3.2 27.1 + - - +
43D LEU* 3.8 22.4 - - + -
133H GLN* 3.3 31.6 + - - +
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C VAL* 4.3 8.7 - - + -
65C ILE* 3.6 44.7 - - + +
78C MET* 3.3 37.2 - - + -
79C ALA* 3.6 20.0 - - + -
82C TYR* 3.9 18.2 - - + -
8D GLN 3.0 11.2 + - - +
9D LYS 3.2 9.2 - - - +
11D LYS* 1.3 76.2 - - - +
13D ALA* 1.3 59.5 + - - +
15D GLN* 3.1 10.0 + - - +
16D ALA* 2.9 26.7 + - - +
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Residues in contact with ALA 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 3.2 31.1 - - + +
9D LYS* 2.8 19.3 + - + +
10D ALA* 3.9 0.4 - - - +
12D LEU* 1.3 70.2 - - - +
14D GLU* 1.3 59.9 + - - +
16D ALA* 3.7 1.6 - - - -
17D GLU 3.0 5.2 + - - -
18D ARG 2.8 45.2 + - - +
21D ASP* 4.0 2.2 - - + -
22D MET* 3.7 21.5 - - + +
25D CYS* 5.7 0.2 - - - -
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Residues in contact with GLU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA 3.1 9.4 + - - +
11D LYS* 3.7 13.4 - - - +
12D LEU 3.2 0.2 - - - -
13D ALA* 1.3 76.5 - - - +
15D GLN* 1.3 66.9 + - + +
17D GLU* 3.2 14.9 + - - +
19D TYR* 3.8 26.7 + - + +
22D MET* 3.5 38.6 - - + +
43D LEU* 4.6 6.6 - - - +
46D VAL* 4.0 6.8 - - + +
35H ASN* 3.2 30.3 + - - +
84H TRP* 4.5 14.7 - - - -
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Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 4.0 16.0 - - + +
65C ILE* 3.6 32.9 - - + +
11D LYS* 3.4 23.3 + - - +
12D LEU* 3.1 9.7 + - - +
14D GLU* 1.3 80.2 - - + +
16D ALA* 1.3 57.4 + - - +
17D GLU* 3.0 18.1 + - - +
84H TRP* 6.5 0.4 - - + -
138H VAL* 3.8 32.5 - - + +
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Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C SER* 2.9 33.0 + - - +
61C VAL* 3.7 22.6 - - + +
62C VAL* 5.1 4.0 - - + -
65C ILE* 5.8 0.2 - - - +
82C TYR* 4.1 12.1 - - + -
86C ILE* 5.0 0.9 - - + -
12D LEU 2.9 16.8 + - - +
13D ALA 4.0 3.1 - - - +
14D GLU 3.3 0.4 - - - -
15D GLN* 1.3 74.5 - - - +
17D GLU* 1.3 67.6 + - - +
18D ARG* 3.4 20.1 + - - -
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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