Contacts of the helix formed by residues 15 - 31 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C ASN* 5.6 4.0 - - + +
11D TYR* 6.0 1.1 - - - +
13D SER* 3.7 7.2 - - - +
14D SER* 1.3 89.3 - - - +
16D HIS* 1.3 65.4 + - - +
17D SER 3.3 2.2 - - - -
18D THR* 2.9 21.6 + - - -
19D ASN* 2.9 35.0 + - - +
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Residues in contact with HIS 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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21C LEU* 3.7 11.4 - - + -
55C CYS* 3.9 14.1 - - - -
90C PHE* 3.2 28.1 + + + -
91C ALA* 2.7 29.2 + - - -
94C ALA* 3.5 32.1 - - + -
116C HIS 5.5 1.1 + - - -
117C ASN* 5.4 6.5 - - + +
13D SER* 2.9 28.6 + - - +
14D SER 3.5 1.4 - - - -
15D VAL* 1.3 76.3 - - - +
17D SER* 1.3 61.7 + - - +
19D ASN* 3.1 13.0 + - - +
20D VAL* 3.1 41.1 + - + +
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Residues in contact with SER 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C SER* 2.7 45.7 + - - +
18C THR* 3.4 16.6 + - - -
21C LEU* 4.2 20.0 - - - +
94C ALA* 4.8 4.3 - - - +
13D SER 5.1 0.6 + - - -
14D SER 4.9 5.2 + - - -
16D HIS* 1.3 82.9 - - - +
18D THR* 1.3 60.5 + - - +
20D VAL* 3.9 5.3 - - - +
21D LEU* 3.3 22.2 + - - +
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Residues in contact with THR 18 (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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17C SER* 3.5 17.9 + - - -
14D SER 4.6 5.2 + - - -
15D VAL* 2.9 15.9 + - - -
17D SER* 1.3 79.2 + - - +
19D ASN* 1.3 61.1 + - - +
21D LEU* 3.5 5.7 + - + +
22D LEU* 3.0 34.1 + - + +
93D THR 6.0 1.3 - - - +
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Residues in contact with ASN 19 (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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117C ASN* 3.7 36.5 - - + +
15D VAL* 2.9 43.0 + - - +
16D HIS* 3.4 10.9 - - - +
18D THR* 1.3 75.8 - - - +
20D VAL* 1.3 60.2 + - + +
22D LEU* 3.4 17.0 + - - +
23D SER* 2.8 34.6 + - - -
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Residues in contact with VAL 20 (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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21C LEU* 4.0 22.9 - - + -
24C LEU* 5.2 2.5 - - + -
51C VAL* 4.6 16.2 - - + -
54C ALA* 4.5 8.2 - - + +
55C CYS* 4.2 13.5 - - - -
91C ALA 4.3 0.4 - - - +
16D HIS* 3.1 45.3 + - + +
17D SER 3.9 5.2 - - - +
19D ASN* 1.3 76.5 - - + +
21D LEU* 1.3 58.3 + - + +
23D SER* 3.2 8.5 + - - -
24D LEU* 2.9 49.7 + - + +
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C HIS* 3.8 24.7 - - + -
17C SER* 4.0 16.4 - - - -
20C VAL* 4.2 25.1 - - + -
17D SER 3.3 14.3 + - - +
18D THR* 3.8 6.7 - - + +
20D VAL* 1.3 80.0 - - + +
22D LEU* 1.3 56.2 + - - +
24D LEU* 3.3 15.7 + - + +
25D ASN 2.9 25.5 + - - -
51D VAL* 5.4 2.2 - - + -
91D ALA 3.7 15.5 - - - +
92D TYR* 3.4 35.3 - - + +
93D THR* 4.2 10.8 - - - +
94D ALA* 4.5 1.8 - - + -
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Residues in contact with LEU 22 (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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18D THR* 3.0 24.8 + - + +
19D ASN* 3.5 17.9 - - - +
21D LEU* 1.3 74.3 - - - +
23D SER* 1.3 57.8 + - - +
25D ASN* 3.3 10.3 + - + +
26D ASP* 3.0 27.6 + - - +
92D TYR 5.0 1.1 - - - -
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Residues in contact with SER 23 (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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54C ALA* 3.4 39.4 + - - +
19D ASN 2.8 17.1 + - - -
20D VAL 3.5 2.5 - - - -
22D LEU* 1.3 73.5 - - - +
24D LEU* 1.3 60.9 + - - +
26D ASP* 3.1 8.5 + - - +
27D GLN* 2.9 35.3 + - - +
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 4.6 12.1 - - + -
50C SER* 3.4 48.0 - - - +
51C VAL* 4.3 8.3 - - + +
54C ALA* 4.9 2.0 - - + -
20D VAL* 2.9 37.0 + - + +
21D LEU* 3.7 16.6 - - + +
23D SER* 1.3 69.6 - - - +
25D ASN* 1.3 61.0 + - - +
27D GLN* 3.4 6.5 + - - +
28D ARG 2.9 22.0 + - - -
48D HIS* 3.4 14.9 - - + +
51D VAL* 3.5 27.1 - - + -
92D TYR* 3.5 15.7 - - + -
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Residues in contact with ASN 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU 2.9 17.3 + - - +
22D LEU* 3.6 9.7 - - + +
24D LEU* 1.3 77.4 - - - +
26D ASP* 1.3 56.8 + - - +
28D ARG* 2.9 37.5 + - - +
29D LYS* 3.0 41.6 + - - +
89D GLN* 6.3 0.4 - - - -
92D TYR* 3.1 25.2 - - + +
93D THR* 3.4 23.8 - - - +
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Residues in contact with ASP 26 (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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22D LEU 3.0 13.4 + - - +
23D SER* 3.1 12.3 + - - +
25D ASN* 1.3 74.2 - - - +
27D GLN* 1.3 65.9 + - + +
29D LYS* 3.5 5.7 + - - +
30D LYS* 3.0 28.6 + - - +
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Residues in contact with GLN 27 (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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50C SER* 3.0 37.9 + - - +
53C ALA* 4.1 7.8 - - - +
54C ALA* 3.9 17.0 - - - +
60C HIS* 5.6 4.7 + - + -
23D SER* 2.9 17.9 + - - +
24D LEU* 3.5 11.7 - - - +
26D ASP* 1.3 75.7 - - + +
28D ARG* 1.3 58.1 + - - +
30D LYS* 3.5 0.6 + - - -
31D ASP 2.8 9.5 + - - -
32D VAL* 2.8 54.9 + - + +
33D LEU* 3.5 13.2 - - + +
34D CYS* 4.0 0.4 - - - -
48D HIS* 2.9 22.8 + - - +
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Residues in contact with ARG 28 (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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24D LEU 2.9 15.3 + - - +
25D ASN* 2.9 38.2 + - - +
27D GLN* 1.3 76.5 - - - +
29D LYS* 1.3 68.6 + - - +
31D ASP* 3.0 19.6 + - - +
34D CYS* 3.8 12.5 - - - -
45D PHE* 5.3 4.9 - - - +
46D ARG* 3.3 32.1 + - - +
85D GLU* 6.0 0.2 + - - -
88D ILE* 4.0 28.3 - - - +
89D GLN* 4.1 31.9 - - - +
92D TYR* 3.5 37.5 - - + +
93D THR* 5.5 0.2 - - - +
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Residues in contact with LYS 29 (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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25D ASN* 3.0 36.1 + - - +
26D ASP* 4.2 7.0 - - - +
27D GLN 3.4 0.2 - - - -
28D ARG* 1.3 88.8 - - - +
30D LYS* 1.3 60.0 + - - +
31D ASP* 3.5 1.9 + - - +
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Residues in contact with LYS 30 (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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26D ASP* 3.0 23.6 + - - +
27D GLN* 4.0 2.5 - - - +
29D LYS* 1.3 74.7 - - - +
31D ASP* 1.3 69.3 + - - +
32D VAL* 4.1 17.1 - - + +
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Residues in contact with ASP 31 (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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27D GLN 2.8 6.0 + - - -
28D ARG 3.0 12.2 + - - +
29D LYS 3.3 2.0 - - - +
30D LYS* 1.3 81.1 - - - +
32D VAL* 1.3 61.5 + - - +
33D LEU 4.3 0.3 + - - -
34D CYS* 4.5 6.8 + - - +
46D ARG* 3.0 47.4 + - + +
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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