Contacts of the helix formed by residues 3 - 16 (chain C) 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 PHE 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER* 1.3 83.3 + - - +
4C ILE* 1.3 62.8 + - - +
5C LYS 3.6 0.4 - - - -
6C PRO* 3.7 11.3 - - - +
7C ILE* 4.0 3.5 + - - +
49C LEU* 3.4 18.3 - - + +
52C LEU* 3.2 24.9 - - + -
117C LEU* 4.3 13.5 - - + -
118C VAL* 3.7 11.7 - - - -
119C LYS* 3.5 44.0 - - + -
122C PHE* 3.8 36.3 - + + -
124C GLU* 3.2 18.2 + - + +
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Residues in contact with ILE 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER* 3.8 1.3 - - - +
3C PHE* 1.3 77.9 - - - +
5C LYS* 1.3 58.4 + - - +
6C PRO* 2.9 4.0 - - - -
7C ILE* 2.9 9.2 + - + -
8C TYR* 2.4 49.8 + - + +
11C ILE* 4.4 5.8 - - + -
45C LEU* 3.4 32.8 - - + -
49C LEU* 4.2 0.7 - - + -
117C LEU* 3.4 26.2 - - + -
124C GLU* 3.9 9.0 - - - +
126C LEU* 4.7 16.2 - - + -
169C LEU* 4.9 9.6 - - + -
187C PHE* 3.4 40.4 - - + -
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Residues in contact with LYS 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER* 2.9 25.5 + - - +
4C ILE* 1.3 77.1 - - - +
6C PRO* 1.3 91.0 - - + +
8C TYR* 2.8 28.3 - - + +
9C GLN* 3.7 2.6 + - - +
187C PHE* 3.5 20.4 - - + -
189C GLU* 4.3 12.1 - - - +
192C LYS* 5.4 6.3 - - - +
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Residues in contact with PRO 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER 4.0 9.9 - - - +
3C PHE* 3.7 15.3 - - - +
4C ILE 3.3 4.0 - - - -
5C LYS* 1.3 110.7 - - + +
7C ILE* 1.3 57.7 + - - +
8C TYR 2.8 10.7 + - - -
9C GLN* 3.4 16.1 + - - +
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Residues in contact with ILE 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE 4.0 1.1 - - - +
4C ILE* 2.9 18.1 + - - +
6C PRO* 1.3 76.0 - - + +
8C TYR* 1.3 59.0 + - - +
9C GLN 3.5 0.4 - - - -
10C ASP* 3.7 13.7 + - + +
11C ILE* 3.0 31.5 + - + +
45C LEU* 5.0 0.2 - - + -
48C ASN* 3.3 34.5 - - + +
49C LEU* 3.5 35.0 - - + -
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Residues in contact with TYR 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 2.4 27.3 + - + +
5C LYS* 2.8 24.5 - - + +
6C PRO 2.8 3.0 + - - -
7C ILE* 1.3 70.8 - - - +
9C GLN* 1.3 64.8 + - - -
10C ASP 2.7 7.0 + - - -
11C ILE* 2.9 27.1 + - + -
12C ASN* 2.8 44.9 + - - +
169C LEU* 3.5 24.9 - - + -
185C THR* 3.1 31.4 + - + -
186C SER* 3.3 6.1 + - - -
187C PHE* 3.7 28.3 - + + -
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Residues in contact with GLN 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LYS 3.7 2.5 + - - +
6C PRO 3.4 12.6 + - - +
8C TYR* 1.3 82.0 - - - +
10C ASP* 1.3 58.1 + - + +
12C ASN* 4.0 12.1 + - - +
13C SER* 4.4 5.7 + - - -
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Residues in contact with ASP 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.7 17.1 + - + +
8C TYR 2.7 4.2 + - - -
9C GLN* 1.3 74.4 - - + +
11C ILE* 1.3 68.0 + - + +
12C ASN 2.8 2.2 - - - -
13C SER* 2.6 24.0 + - - -
14C ILE* 3.3 10.0 + - + -
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Residues in contact with ILE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 4.4 7.4 - - + -
7C ILE* 3.0 35.0 - - + +
8C TYR* 2.9 28.2 + - + +
10C ASP* 1.3 76.7 - - - +
12C ASN* 1.3 64.9 + - - +
14C ILE* 2.8 27.7 - - + +
15C LEU* 3.3 28.5 + - + +
41C VAL* 5.3 3.6 - - + -
44C PHE* 5.2 13.5 - - + +
45C LEU* 3.6 33.2 - - + +
48C ASN* 5.9 1.1 - - + -
169C LEU* 4.8 10.8 - - + -
185C THR* 5.6 0.4 - - + -
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Residues in contact with ASN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C TYR* 2.8 43.6 + - - +
9C GLN* 4.0 13.9 + - - +
10C ASP 2.6 4.4 + - - -
11C ILE* 1.3 75.1 - - - +
13C SER* 1.3 57.7 + - - +
15C LEU* 3.9 1.6 - - - +
16C ILE* 3.0 45.8 + - + +
185C THR* 2.9 42.2 + - - +
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Residues in contact with SER 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLN 4.4 7.3 + - - -
10C ASP* 2.6 16.1 + - - -
12C ASN* 1.3 73.0 - - - +
14C ILE* 1.3 62.6 + - - +
15C LEU 3.3 0.3 + - - -
16C ILE* 3.6 23.0 + - - +
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Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASP 3.3 3.8 + - - +
11C ILE* 2.8 40.8 - - + +
13C SER* 1.3 77.6 - - - +
15C LEU* 1.3 66.5 + - + +
16C ILE 4.9 0.5 - - - +
18C GLN* 2.6 55.1 + - - +
44C PHE* 4.3 19.7 - - + -
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.3 30.6 + - + +
12C ASN 3.9 1.6 - - - +
13C SER 3.2 0.4 - - - -
14C ILE* 1.3 88.8 - - + +
16C ILE* 1.3 53.3 + - - +
17C GLY 2.6 19.6 + - - -
18C GLN* 2.7 46.6 + - + +
37C PHE* 6.1 1.3 - - + -
40C LEU* 3.7 24.9 - - + +
41C VAL* 3.4 26.7 - - + -
44C PHE* 5.0 1.1 - - + -
169C LEU* 4.8 5.6 - - + -
171C VAL* 5.0 9.9 - - + -
182C CYS* 3.5 17.6 - - + +
185C THR* 4.8 9.9 - - + +
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Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASN* 3.0 36.2 + - + +
13C SER* 3.6 15.8 + - - +
14C ILE 4.9 1.0 - - - +
15C LEU* 1.3 71.2 - - - +
17C GLY* 1.3 59.7 + - - +
182C CYS* 4.0 12.5 - - - +
183C VAL* 4.1 34.5 - - - +
184C SER* 4.2 7.0 - - - +
185C THR* 4.2 4.0 - - - +
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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