Contacts of the helix formed by residues 39 - 53 (chain D) in PDB entry 2H4C
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 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D TYR* 2.9 25.9 + - - -
37D PRO 3.1 3.5 + - - -
38D LYS* 1.3 82.8 - - - +
40D ALA* 1.3 58.4 + - + +
41D THR* 3.4 7.0 + - - -
42D ASP* 2.7 45.1 + - - +
43D ARG* 2.7 17.6 + - - +
112D THR* 3.8 18.3 + - - +
114D ASP* 4.2 2.3 + - - +
117D TYR* 3.7 13.0 - - + -
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Residues in contact with ALA 40 (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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39D ASP* 1.3 72.9 - - - +
41D THR* 1.3 62.1 + - - +
43D ARG* 3.2 10.0 - - - +
44D CYS* 3.1 23.4 + - - -
105D CYS* 4.5 0.3 - - - -
109D ASN* 3.3 36.9 + - + +
112D THR* 3.4 17.0 - - + +
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Residues in contact with THR 41 (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 TYR* 3.8 16.2 + - + -
25D TYR* 3.7 26.9 - - + -
29D CYS* 4.0 3.8 - - - -
39D ASP* 2.9 12.8 + - - -
40D ALA* 1.3 74.0 - - - +
42D ASP* 1.3 70.4 + - - +
44D CYS* 2.6 31.1 + - - +
45D CYS 3.1 2.6 + - - -
106D PHE* 3.4 24.4 - - + -
109D ASN* 3.8 20.6 + - - +
110D MET* 4.9 1.4 + - - -
112D THR* 4.2 2.2 + - - -
113D TYR* 4.5 11.4 - - + +
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Residues in contact with ASP 42 (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 TYR* 3.1 25.4 - - + +
26D GLY* 3.5 4.9 - - - -
27D CYS* 2.8 23.5 + - - +
28D TYR* 3.2 14.1 + - - -
29D CYS* 3.5 8.8 + - - -
37D PRO* 3.3 10.6 - - - +
38D LYS* 2.8 21.7 + - + +
39D ASP* 2.7 33.8 + - - +
41D THR* 1.3 71.7 - - - +
43D ARG* 1.3 51.9 + - - +
45D CYS* 2.7 6.9 + - - +
46D PHE* 2.6 32.7 + - - +
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Residues in contact with ARG 43 (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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36D THR* 5.8 0.2 - - - +
37D PRO* 3.9 18.2 - - + +
39D ASP 2.7 16.3 + - - +
40D ALA* 3.2 14.6 - - - +
42D ASP* 1.3 70.6 - - - +
44D CYS* 1.3 65.9 + - - +
46D PHE* 2.7 46.5 + - - -
47D VAL* 2.9 31.2 + - + +
131D ASP* 3.0 33.5 + - - -
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Residues in contact with CYS 44 (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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40D ALA 3.1 6.4 + - - -
41D THR* 2.6 17.6 + - - +
43D ARG* 1.3 76.1 - - - +
45D CYS* 1.3 54.6 + - - +
47D VAL* 3.9 4.3 + - - +
48D HIS* 3.1 24.8 + - - +
102D ALA* 4.2 7.5 - - - +
105D CYS* 2.0 72.2 - - + -
106D PHE* 3.3 24.5 - - + -
109D ASN* 3.4 12.3 - - - -
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Residues in contact with CYS 45 (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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31C TRP* 6.5 0.7 - - - -
5D PHE* 5.9 5.2 - - - -
22D TYR* 4.8 3.6 - - - -
28D TYR 4.1 1.6 - - - -
29D CYS* 2.0 66.0 - - - +
30D GLY 4.7 1.3 - - - -
41D THR 3.1 1.0 + - - -
42D ASP 2.7 11.4 + - - +
44D CYS* 1.3 73.6 - - - +
46D PHE* 1.3 67.8 + - - +
48D HIS* 2.8 17.4 + - - +
49D ASP* 3.0 19.0 + - - +
106D PHE* 3.2 22.9 - - - -
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Residues in contact with PHE 46 (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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70C MET* 4.0 2.5 - - + -
28D TYR* 3.3 42.2 - + + +
37D PRO* 3.5 21.5 - - + -
42D ASP 2.6 13.0 + - - +
43D ARG* 2.7 39.7 + - - +
45D CYS* 1.3 74.3 - - - +
47D VAL* 1.3 78.0 - - + +
49D ASP* 3.1 12.2 + - - +
50D CYS* 3.2 38.0 + - - +
131D ASP* 3.2 44.6 - - + -
132D GLN 3.7 10.1 - - - -
133D CYS* 4.4 6.7 - - - -
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Residues in contact with VAL 47 (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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43D ARG* 2.9 31.8 + - + +
44D CYS* 4.2 3.8 - - - +
46D PHE* 1.3 95.0 - - + +
48D HIS* 1.3 66.0 + - - +
50D CYS* 3.4 7.3 + - + +
51D CYS* 2.8 25.3 + - + +
101D VAL* 6.4 1.6 - - + -
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Residues in contact with HIS 48 (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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69C LYS* 4.3 6.7 + - - -
2D LEU* 5.1 0.9 - - + -
5D PHE* 3.5 25.6 - + + -
44D CYS 3.1 16.8 + - - +
45D CYS* 2.8 14.8 + - - +
47D VAL* 1.3 76.4 - - - +
49D ASP* 1.3 73.4 + - - +
51D CYS* 2.9 21.7 + - - +
52D TYR* 3.1 40.2 + + - -
98D CYS* 3.0 30.1 - - + -
99D ASP* 2.5 23.7 + - - -
102D ALA* 3.3 17.7 - - + -
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Residues in contact with ASP 49 (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 ASN* 5.6 1.8 + - - +
69C LYS* 2.8 48.3 + - + +
70C MET* 3.5 23.1 - - - -
28D TYR* 3.9 27.5 - - - +
30D GLY 5.7 0.3 - - - +
33D GLY* 5.2 2.7 - - - -
45D CYS* 3.0 24.3 + - - +
46D PHE 3.4 5.8 - - - +
48D HIS* 1.3 79.7 + - - +
50D CYS* 1.3 56.1 + - - +
51D CYS 2.7 10.9 + - - -
52D TYR* 2.8 18.9 + - - +
53D ALA* 3.2 9.2 + - - +
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Residues in contact with CYS 50 (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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70C MET* 3.3 21.3 - - - -
46D PHE* 3.2 20.0 + - + +
47D VAL* 3.8 11.9 - - + +
49D ASP* 1.3 77.0 - - - +
51D CYS* 1.3 59.0 + - - +
53D ALA* 3.4 12.5 - - - +
54D ARG* 3.4 27.0 + - - +
133D CYS* 2.0 63.0 - - + +
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Residues in contact with CYS 51 (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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47D VAL* 2.8 17.9 + - + +
48D HIS* 2.9 16.2 - - - +
49D ASP 2.7 2.2 + - - -
50D CYS* 1.3 76.4 - - - +
52D TYR* 1.3 62.5 + - - +
53D ALA 3.2 0.2 - - - -
54D ARG* 3.1 23.4 + - - +
55D VAL* 3.9 0.7 - - - +
94D ALA 4.5 1.1 - - - -
97D GLU* 5.7 0.7 - - - -
98D CYS* 2.0 64.1 - - + +
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Residues in contact with TYR 52 (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 ASN* 4.9 8.5 - - - +
69C LYS* 4.2 24.9 - - + -
1D ASN 5.1 0.9 + - - -
2D LEU* 3.7 21.3 - - + +
48D HIS* 3.1 28.1 + + - -
49D ASP* 2.8 11.2 + - - +
51D CYS* 1.3 72.8 - - - +
53D ALA* 1.3 53.5 + - - +
54D ARG 2.5 13.7 + - - -
55D VAL* 2.8 24.2 + - - +
68D PRO* 3.3 49.3 + - + +
69D LYS* 5.4 1.6 - - + -
95D VAL* 3.8 13.7 - - + -
98D CYS* 3.3 19.2 - - + -
99D ASP* 2.6 41.3 + - - -
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Residues in contact with ALA 53 (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 ASN* 4.3 28.8 - - + +
70C MET* 5.5 4.5 - - + -
49D ASP 3.2 7.2 + - - +
50D CYS* 3.4 19.7 - - - +
52D TYR* 1.3 76.5 - - - +
54D ARG* 1.3 59.0 + - + +
55D VAL 3.5 4.2 + - - +
133D CYS* 5.3 5.2 - - - -
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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