Contacts of the helix formed by residues 15 - 31 (chain C) in PDB entry 2IHC
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 VAL 15 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 4.9 15.0 - - + -
121A SER* 5.1 4.5 - - - -
122A CYS* 4.0 18.4 - - + +
125A PHE* 3.1 40.8 - - + -
9B PHE* 4.5 4.3 - - + -
11B TYR* 5.1 5.4 - - + -
11C TYR* 5.9 0.4 - - - +
13C SER* 3.3 13.5 - - - +
14C SER* 1.3 82.5 - - - +
16C HIS* 1.3 57.5 + - - +
17C SER 3.5 2.5 - - - -
18C THR* 3.6 5.0 + - - -
19C ASN* 3.0 31.5 + - - +
117D ASN* 4.2 20.2 - - + +
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Residues in contact with HIS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 3.1 27.0 + - - +
14C SER 3.7 1.0 - - - -
15C VAL* 1.3 77.6 - - - +
17C SER* 1.3 59.3 + - - +
19C ASN* 3.1 3.6 + - - +
20C VAL* 2.8 46.2 + - + +
21D LEU* 3.8 17.5 - - + -
55D CYS* 3.6 20.6 - - + -
90D PHE* 3.5 34.5 + + + -
91D ALA* 2.9 27.2 + - - -
94D ALA* 3.9 9.9 - - + -
116D HIS 5.2 0.9 - - - -
117D ASN* 3.4 25.7 + - - +
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Residues in contact with SER 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER 5.3 0.8 + - - -
14C SER 5.3 3.8 + - - -
15C VAL 3.5 0.6 - - - -
16C HIS* 1.3 74.6 - - - +
18C THR* 1.3 69.4 + - - +
19C ASN 3.0 1.3 - - - -
20C VAL* 3.1 5.5 + - - +
21C LEU* 2.9 26.0 + - - +
17D SER* 2.7 43.6 + - - +
18D THR* 3.5 16.1 + - - -
21D LEU* 4.0 22.2 - - - -
94D ALA* 4.9 5.9 - - - +
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Residues in contact with THR 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 3.6 24.9 - - + -
0B MET* 3.5 31.2 - - + +
9B PHE* 4.1 14.3 - - - -
14C SER 4.7 2.8 + - - -
15C VAL 3.6 10.0 + - - -
17C SER* 1.3 81.9 + - - +
19C ASN* 1.3 56.8 + - - +
21C LEU* 3.7 2.5 + - - +
22C LEU* 3.1 36.8 + - + +
17D SER* 3.7 15.7 + - - -
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Residues in contact with ASN 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER* 5.2 7.9 - - - -
125A PHE* 3.7 20.6 - - - -
15C VAL* 3.0 28.0 + - - +
16C HIS 3.3 8.5 - - - +
17C SER 3.0 0.2 - - - -
18C THR* 1.3 76.2 - - - +
20C VAL* 1.3 60.1 + - + +
22C LEU* 3.4 8.9 + - - +
23C SER* 2.9 33.5 + - - +
117D ASN* 2.7 38.3 + - - +
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C HIS* 2.8 53.6 + - + +
17C SER 3.1 5.1 + - - +
19C ASN* 1.3 68.7 - - + +
21C LEU* 1.3 66.4 + - - +
23C SER* 3.2 7.2 + - - -
24C LEU* 2.9 43.1 + - + +
20D VAL* 6.5 0.2 - - + -
21D LEU* 4.2 21.8 - - + -
51D VAL* 4.8 11.0 - - + -
54D ALA* 4.5 13.9 - - + -
55D CYS* 3.9 14.1 - - - -
117D ASN* 5.6 0.7 - - - +
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Residues in contact with LEU 21 (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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17C SER 2.9 15.2 + - - +
18C THR* 4.0 3.8 - - - +
20C VAL* 1.3 75.2 - - - +
22C LEU* 1.3 57.2 + - - +
24C LEU* 3.2 13.4 + - + +
25C ASN* 2.8 30.3 + - - +
51C VAL* 5.2 4.0 - - + -
91C ALA 3.8 14.4 - - - +
92C TYR* 3.2 36.3 - - + +
93C THR* 3.8 11.9 - - - +
94C ALA* 4.4 1.3 - - + -
16D HIS* 3.7 23.1 - - + -
17D SER* 4.2 15.3 - - - +
20D VAL* 4.0 29.8 - - + -
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 3.5 35.4 - - + -
0B MET* 5.6 3.1 - - + -
18C THR* 3.1 32.4 + - + +
19C ASN* 3.6 12.8 - - - +
20C VAL 3.3 0.2 - - - -
21C LEU* 1.3 77.1 - - - +
23C SER* 1.3 57.3 + - - +
25C ASN* 3.4 9.2 + - + +
26C ASP* 2.9 27.1 + - - +
92C TYR 5.1 1.1 - - - -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASN* 2.9 19.2 + - - +
20C VAL* 3.2 3.7 + - - -
22C LEU* 1.3 73.3 - - - +
24C LEU* 1.3 60.3 + - - +
26C ASP* 3.1 8.8 + - - +
27C GLN* 2.8 37.6 + - - +
54D ALA* 3.9 30.4 + - - +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 2.9 40.7 + - + +
21C LEU* 3.5 16.8 - - + +
23C SER* 1.3 71.2 - - - +
25C ASN* 1.3 61.2 + - - +
27C GLN* 3.4 7.0 + - - +
28C ARG* 2.9 24.8 + - - +
48C HIS* 3.4 24.0 - - + +
51C VAL* 4.3 18.6 - - + -
92C TYR* 3.7 14.5 - - + -
20D VAL* 5.2 1.3 - - + -
24D LEU* 4.6 11.0 - - + -
50D SER* 3.7 40.4 - - - +
51D VAL* 4.7 3.4 - - + +
54D ALA* 5.2 1.1 - - + -
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Residues in contact with ASN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU 2.8 18.1 + - - +
22C LEU* 3.6 9.5 - - + +
24C LEU* 1.3 77.5 - - - +
26C ASP* 1.3 56.6 + - - +
28C ARG* 3.2 5.4 + - - +
29C LYS* 2.9 32.7 + - - +
89C GLN* 5.8 0.9 - - - -
92C TYR* 3.2 38.6 - - + +
93C THR* 3.6 20.2 - - - +
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Residues in contact with ASP 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU 2.9 15.3 + - - +
23C SER* 3.1 11.8 + - - +
25C ASN* 1.3 73.2 - - - +
27C GLN* 1.3 66.2 + - + +
29C LYS* 3.5 6.0 + - - +
30C LYS* 3.0 36.2 + - - +
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Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER* 2.8 19.1 + - - +
24C LEU* 3.5 11.0 - - - +
26C ASP* 1.3 77.4 - - + +
28C ARG* 1.3 56.6 + - - +
30C LYS* 3.6 0.6 - - - -
31C ASP 2.9 8.8 + - - -
32C VAL* 2.8 55.3 + - + +
33C LEU* 3.4 26.8 - - - +
34C CYS* 4.4 0.2 - - - -
48C HIS* 3.2 21.6 + - - +
50D SER* 3.2 34.8 + - - -
53D ALA* 3.9 7.1 - - - +
54D ALA* 4.0 10.1 - - - +
60D HIS* 5.3 4.9 + - + -
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Residues in contact with ARG 28 (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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24C LEU 2.9 14.6 + - - +
25C ASN* 3.2 17.5 + - - +
27C GLN* 1.3 75.9 - - - +
29C LYS* 1.3 62.3 + - - +
31C ASP* 3.1 15.2 + - - +
34C CYS* 3.7 16.8 - - - -
46C ARG* 4.4 19.1 - - - +
48C HIS* 4.3 0.9 - - + -
92C TYR* 4.2 18.8 - - + -
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Residues in contact with LYS 29 (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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25C ASN* 2.9 20.7 + - - +
26C ASP* 4.0 7.6 - - - +
28C ARG* 1.3 76.6 - - - +
30C LYS* 1.3 61.6 + - + +
31C ASP* 3.2 2.1 + - - +
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Residues in contact with LYS 30 (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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26C ASP* 3.0 28.8 + - - +
27C GLN* 4.2 2.0 - - - +
29C LYS* 1.3 75.7 - - + +
31C ASP* 1.3 69.1 + - - +
32C VAL* 4.5 15.5 - - + +
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Residues in contact with ASP 31 (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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27C GLN 2.9 6.0 + - - -
28C ARG 3.1 12.8 + - - +
29C LYS 3.2 1.7 - - - +
30C LYS* 1.3 80.4 - - - +
32C VAL* 1.3 58.9 + - - +
33C LEU 4.3 0.7 + - - -
34C CYS* 4.6 12.4 + - - +
46C ARG* 6.5 0.9 - - - +
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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