Contacts of the helix formed by residues 44 - 59 (chain D) in PDB entry 1D7G
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 SER 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B G 3.5 38.7 + - - -
9B C 3.9 11.2 + - - -
43D ALA* 1.3 75.1 - - - +
45D VAL* 1.3 62.8 + - - +
46D MET* 3.1 30.0 + - - -
47D ARG* 3.2 19.7 + - - +
48D LEU* 3.6 15.7 - - - +
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Residues in contact with VAL 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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9B C 4.8 9.5 + - - +
23D PHE* 4.0 40.4 - - + +
26D LEU* 4.5 8.3 - - + -
27D ALA* 4.3 24.5 - - + -
30D LEU* 5.2 1.9 - - + +
44D SER* 1.3 69.3 - - - +
46D MET* 1.3 62.2 + - + +
47D ARG 3.4 0.2 - - - -
48D LEU* 3.4 19.2 + - + +
49D THR* 2.9 34.9 + - - +
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Residues in contact with MET 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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9B C 4.6 8.1 - - - +
19C MET* 3.9 26.9 - - + -
22C TYR* 3.4 49.4 - - + -
23D PHE* 3.6 36.6 - - + -
26D LEU* 5.6 3.4 - - + -
44D SER* 4.0 22.7 - - - -
45D VAL* 1.3 80.5 - - + +
47D ARG* 1.3 64.7 + - + +
49D THR* 3.4 7.4 + - - -
50D ILE* 3.2 34.1 + - + +
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Residues in contact with ARG 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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7B A 5.5 0.4 + - - -
8B G 4.3 11.1 + - - -
39D HIS* 5.4 0.4 - - - -
40D LEU* 4.2 23.3 - - + +
41D ASP* 3.2 37.0 + - - -
43D ALA* 3.7 20.8 - - - +
44D SER* 3.2 13.7 + - - +
46D MET* 1.3 74.1 - - + +
48D LEU* 1.3 68.0 + - + +
50D ILE* 3.4 10.2 + - + +
51D SER* 2.9 31.2 + - - +
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Residues in contact with LEU 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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30D LEU* 4.1 31.2 - - + -
34D HIS* 6.0 4.3 - - + -
38D SER* 6.0 0.2 - - - +
39D HIS* 3.8 40.6 + - + -
40D LEU 5.1 0.4 - - - +
42D LYS* 4.1 38.6 - - + -
43D ALA 4.7 0.2 - - - +
44D SER 3.6 15.5 - - - +
45D VAL* 3.4 19.9 + - + +
47D ARG* 1.3 77.5 - - + +
49D THR* 1.3 57.2 + - - +
51D SER* 3.6 1.4 + - - -
52D TYR* 2.9 32.0 + - - +
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Residues in contact with THR 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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53C MET* 5.8 1.3 - - + -
26D LEU* 3.3 42.9 - - + +
30D LEU* 4.6 7.7 - - - +
45D VAL 2.9 17.8 + - - -
46D MET* 3.5 8.7 - - - +
48D LEU* 1.3 72.5 - - - +
50D ILE* 1.3 68.0 + - + +
52D TYR* 3.3 5.6 + - - +
53D LEU* 3.0 48.5 + - + +
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Residues in contact with ILE 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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22C TYR* 5.6 10.1 - - + -
25C GLU* 5.2 9.6 - - - +
46D MET* 3.2 24.5 + - + +
47D ARG* 3.8 8.1 - - + +
49D THR* 1.3 77.8 - - + +
51D SER* 1.3 63.7 + - - +
53D LEU* 3.8 8.1 - - + +
54D ARG* 3.1 39.9 + - + +
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Residues in contact with SER 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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39D HIS* 3.5 25.1 - - - +
40D LEU* 4.2 22.1 + - - +
47D ARG* 2.9 20.0 + - - +
50D ILE* 1.3 77.2 - - - +
52D TYR* 1.3 64.5 + - - +
54D ARG* 3.4 6.3 + - - +
55D VAL* 3.4 25.6 + - - +
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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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57C ARG* 6.4 0.2 - - - -
29D GLN* 3.8 22.8 + - + +
30D LEU* 3.7 33.2 + - + -
33D PRO* 3.9 13.2 - - + +
39D HIS* 4.0 9.6 - + + -
48D LEU 2.9 19.9 + - - +
49D THR* 3.6 6.3 - - - +
51D SER* 1.3 74.5 - - - +
53D LEU* 1.3 72.9 + - + +
55D VAL* 3.3 9.0 + - - +
56D ARG* 3.2 79.1 + - + +
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Residues in contact with LEU 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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29C MET* 4.3 26.0 - - + -
53C MET* 5.9 7.0 - - + -
56C LEU* 6.2 4.0 - - + -
57C ARG* 6.0 5.2 - - - +
49D THR* 3.0 40.4 + - + +
50D ILE* 3.8 7.9 - - + +
52D TYR* 1.3 83.8 - - + +
54D ARG* 1.3 52.3 + - + +
56D ARG* 3.3 6.7 + - + +
57D LYS* 2.8 38.0 + - + +
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Residues in contact with ARG 54 (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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50D ILE* 3.1 32.7 + - + +
51D SER* 3.6 7.6 - - - +
52D TYR 3.4 0.4 - - - -
53D LEU* 1.3 74.1 - - + +
55D VAL* 1.3 62.5 + - + +
57D LYS* 3.6 30.4 - - - +
58D LEU* 3.1 72.6 + - + +
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Residues in contact with VAL 55 (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 HIS* 6.5 0.4 - - + -
51D SER 3.4 14.3 + - - +
52D TYR 3.3 8.2 + - - +
54D ARG* 1.3 76.8 - - + +
56D ARG* 1.3 78.3 - - - +
58D LEU* 3.5 7.3 + - - +
59D LEU* 3.0 33.8 + - + +
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Residues in contact with ARG 56 (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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32D LEU* 6.4 0.2 - - - +
33D PRO* 4.2 14.6 - - - +
39D HIS* 5.1 3.0 - - - -
52D TYR* 3.2 76.8 + - + +
53D LEU* 3.3 9.0 + - + +
55D VAL* 1.3 95.9 - - - +
57D LYS* 1.3 59.6 + - - +
59D LEU* 3.0 37.8 - - + +
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Residues in contact with LYS 57 (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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53D LEU 2.8 19.5 + - - +
54D ARG* 3.6 26.5 - - - +
56D ARG* 1.3 75.7 - - - +
58D LEU* 1.3 64.2 + - - +
59D LEU 3.7 4.2 - - - +
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Residues in contact with LEU 58 (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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54D ARG* 3.1 53.4 + - + +
55D VAL* 3.8 6.3 - - - +
57D LYS* 1.3 71.6 - - - +
59D LEU* 1.3 66.9 + - - +
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Residues in contact with LEU 59 (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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55D VAL* 3.0 22.9 + - + +
56D ARG* 3.0 33.7 - - + +
57D LYS 3.4 4.8 - - - +
58D LEU* 1.3 79.7 - - - +
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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