Contacts of the helix formed by residues 4 - 16 (chain D) in PDB entry 1XHU
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 ILE 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D PHE* 1.3 78.5 - - - +
5D LYS* 1.3 54.5 + - - +
7D ILE* 2.9 11.8 + - + +
8D TYR* 2.6 36.9 + - + -
11D ILE* 4.7 18.4 - - + -
45D LEU* 4.3 24.5 - - + -
117D LEU* 3.4 15.0 - - + -
124D GLU* 3.1 24.0 - - - +
126D LEU* 3.4 40.4 - - + -
167D ASN* 4.5 0.7 - - + -
169D LEU* 5.5 3.6 - - + -
187D PHE* 3.4 28.9 - - + -
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Residues in contact with LYS 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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2D SER* 3.2 14.6 + - - +
4D ILE* 1.3 79.1 - - - +
6D PRO* 1.3 64.5 - - + +
8D TYR* 2.7 34.6 + - - +
9D GLN* 3.3 8.1 + - - +
187D PHE* 4.0 19.0 - - + -
189D GLU* 5.4 1.8 - - - +
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Residues in contact with PRO 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 SER 3.7 15.7 - - - +
3D PHE* 3.4 17.9 - - + +
4D ILE 3.4 3.8 - - - -
5D LYS* 1.3 94.8 - - + +
7D ILE* 1.3 62.0 + - + +
9D GLN* 3.5 18.5 + - - +
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Residues in contact with ILE 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 PHE 4.1 13.2 - - - +
4D ILE* 2.9 14.5 + - + +
5D LYS 2.8 0.4 + - - -
6D PRO* 1.3 81.7 - - + +
8D TYR* 1.3 67.3 + - - +
9D GLN* 3.3 3.4 - - - -
10D ASP* 2.9 27.8 + - + +
11D ILE* 3.2 11.2 + - + +
44D PHE* 3.5 17.0 - - + -
45D LEU* 5.6 5.4 - - + -
48D ASN* 3.5 34.5 - - + +
49D LEU* 5.1 17.7 - - + -
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Residues in contact with TYR 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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4D ILE* 2.6 18.9 + - + +
5D LYS* 2.7 21.9 + - - +
7D ILE* 1.3 72.6 - - - +
9D GLN* 1.3 62.8 + - - +
10D ASP 2.7 0.9 + - - -
11D ILE* 3.0 15.2 + - + -
12D ASN* 2.6 53.8 + - + +
169D LEU* 3.4 26.5 - - + -
185D THR* 2.5 32.1 + - - -
186D SER* 2.8 16.8 + - - -
187D PHE* 3.5 27.4 - + + -
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Residues in contact with GLN 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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5D LYS 3.3 12.4 + - - +
6D PRO* 3.5 21.7 + - - +
7D ILE 4.3 2.5 - - - -
8D TYR* 1.3 78.4 - - - +
10D ASP* 1.3 72.6 + - - +
12D ASN* 4.0 6.7 - - - +
13D SER* 3.6 17.2 + - - -
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Residues in contact with ASP 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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7D ILE* 2.9 27.0 + - + +
8D TYR 2.7 3.8 + - - -
9D GLN* 1.3 80.3 - - - +
11D ILE* 1.3 64.6 + - - +
12D ASN 3.1 0.9 - - - -
13D SER* 2.5 26.5 + - - -
14D ILE* 2.6 22.2 - - + +
44D PHE* 4.2 5.4 - - + -
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Residues in contact with ILE 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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4D ILE* 4.7 9.2 - - + -
7D ILE* 3.2 8.2 + - + +
8D TYR* 3.1 34.8 - - + +
10D ASP* 1.3 78.7 - - - +
12D ASN* 1.3 60.0 + - - +
14D ILE* 3.9 1.7 - - + +
15D LEU* 2.8 51.4 + - + +
41D VAL* 3.8 31.6 - - + +
44D PHE* 3.4 34.2 - - + -
45D LEU* 4.0 20.2 - - + -
169D LEU* 4.2 8.5 - - + -
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Residues in contact with ASN 12 (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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8D TYR* 2.6 44.6 + - + +
9D GLN* 4.0 7.0 - - - +
11D ILE* 1.3 75.4 - - - +
13D SER* 1.3 56.6 - - - +
15D LEU* 4.6 1.1 - - - -
16D ILE* 3.3 30.7 + - + +
185D THR* 3.5 24.9 + - - +
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Residues in contact with SER 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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9D GLN 3.6 10.7 + - - -
10D ASP* 2.5 23.2 + - - -
12D ASN* 1.3 77.6 - - - +
14D ILE* 1.3 77.4 + - - +
15D LEU 2.9 1.8 - - - -
16D ILE* 2.9 29.3 + - - +
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Residues in contact with ILE 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 ASP* 2.6 42.7 + - + +
11D ILE* 3.9 5.2 - - + +
13D SER* 1.3 88.1 + - - +
15D LEU* 1.3 53.6 + - + +
16D ILE 3.5 0.7 + - - +
18D GLN* 2.6 35.7 - - - +
40D LEU* 6.6 0.4 - - + -
44D PHE* 3.4 48.2 - - + -
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Residues in contact with LEU 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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11D ILE* 2.8 35.7 + - + +
12D ASN* 4.0 0.7 - - - +
14D ILE* 1.3 78.8 - - + +
16D ILE* 1.3 60.8 + - - +
17D GLY 3.4 2.9 + - - -
18D GLN* 3.4 15.0 + - - +
37D PHE* 5.1 5.5 - - + +
40D LEU* 5.3 15.9 - - + +
41D VAL* 3.8 26.9 - - + +
44D PHE* 6.5 0.9 - - + -
169D LEU* 3.5 32.1 - - + -
171D VAL* 4.4 11.7 - - + -
182D CYS* 3.5 14.7 - - - +
185D THR* 3.6 32.1 - - + -
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Residues in contact with ILE 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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12D ASN* 3.3 20.0 - - + +
13D SER* 2.9 19.2 + - - +
14D ILE 3.9 2.8 - - - +
15D LEU* 1.3 74.7 - - - +
17D GLY* 1.3 58.9 + - - +
18D GLN* 3.9 1.2 - - - +
182D CYS* 3.0 35.7 - - - +
183D VAL* 3.4 22.0 - - - +
184D SER* 3.8 10.1 - - - +
185D THR* 3.9 7.0 - - + +
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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