Contacts of the helix formed by residues 38 - 53 (chain D) in PDB entry 6R7H
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 GLY 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D SER* 1.3 78.5 - - - +
39D ALA* 1.3 63.0 + - - -
40D GLU 3.4 0.2 + - - -
41D GLN* 3.5 14.6 + - - +
42D LEU* 4.1 4.5 + - - +
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Residues in contact with ALA 39 (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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38D GLY* 1.3 70.9 - - - -
40D GLU* 1.3 71.5 + - - +
41D GLN 3.3 0.9 + - - -
42D LEU* 3.6 7.9 + - - +
43D GLU* 3.5 25.8 + - + +
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Residues in contact with GLU 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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1D MET* 3.1 17.2 + - + +
2D ALA* 2.9 39.8 + - - +
36D LEU* 4.0 20.4 - - + +
37D SER 4.0 9.6 - - - +
38D GLY 3.2 0.8 - - - -
39D ALA* 1.3 86.1 - - + +
41D GLN* 1.3 62.6 + - - +
43D GLU* 4.1 3.6 - - - +
44D ALA* 3.2 24.6 + - - +
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Residues in contact with GLN 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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33D ALA 3.7 12.1 - - - +
34D ILE* 3.3 14.6 - - - +
36D LEU* 3.0 36.3 + - - +
37D SER* 3.8 8.6 + - - +
38D GLY 3.5 13.0 + - - +
39D ALA 3.3 0.8 - - - -
40D GLU* 1.3 77.7 - - - +
42D LEU* 1.3 64.6 + - - +
44D ALA* 3.5 1.3 + - - +
45D LEU* 3.1 40.1 + - + +
76D LEU* 4.1 20.5 - - - +
77D PRO* 6.4 0.2 - - - +
80D THR* 4.4 19.3 + - + +
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Residues in contact with LEU 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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38D GLY 4.1 4.9 + - - +
39D ALA* 3.6 10.4 + - - +
40D GLU 3.4 0.2 - - - -
41D GLN* 1.3 78.9 - - - +
43D GLU* 1.3 69.9 + - - +
45D LEU* 3.7 3.1 + - - +
46D LYS* 3.3 52.8 + - + +
80D THR* 3.8 36.6 - - + +
83D GLU* 3.9 23.1 - - + +
84D ILE* 4.4 14.8 - - + -
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Residues in contact with GLU 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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2D ALA* 4.1 21.9 - - + +
6D ARG* 3.5 37.2 + - - +
39D ALA* 3.5 17.0 + - + +
40D GLU* 4.3 2.7 - - - +
41D GLN 3.3 0.4 - - - -
42D LEU* 1.3 85.8 - - + +
44D ALA* 1.3 60.0 + - - +
46D LYS* 4.1 13.7 - - - +
47D ALA* 3.6 15.9 + - - +
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Residues in contact with ALA 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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2D ALA* 4.9 4.0 - - + +
5D VAL* 4.1 32.4 - - + +
9D LEU* 5.2 0.5 - - - +
30D LEU* 5.7 0.2 - - - +
33D ALA* 3.7 28.1 - - + +
36D LEU* 4.4 5.2 - - + -
40D GLU 3.2 19.1 + - - +
41D GLN* 4.0 2.5 - - - +
42D LEU 3.3 0.2 - - - -
43D GLU* 1.3 77.4 - - - +
45D LEU* 1.3 64.2 + - - +
47D ALA* 3.5 10.7 + - - +
48D PHE* 3.7 10.7 + - - +
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Residues in contact with LEU 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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30D LEU* 4.4 8.7 - - + -
33D ALA* 4.3 21.3 - - + +
34D ILE* 4.8 10.3 - - + -
41D GLN* 3.1 40.4 + - + +
42D LEU* 4.3 3.8 - - - +
44D ALA* 1.3 76.2 - - - +
46D LYS* 1.3 62.7 + - + +
48D PHE* 3.4 16.5 + - - +
49D VAL* 3.9 11.4 + - - +
69D PHE* 3.7 32.2 - - + -
73D LEU* 5.5 0.2 - - + -
76D LEU* 4.1 15.9 - - + -
80D THR* 5.8 1.6 - - + -
84D ILE* 3.9 32.7 - - + +
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Residues in contact with LYS 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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6D ARG* 5.2 4.3 - - - +
42D LEU* 3.3 44.3 + - + +
43D GLU* 4.4 15.7 - - - +
44D ALA 3.3 0.2 - - - -
45D LEU* 1.3 75.8 - - + +
47D ALA* 1.3 63.6 + - - +
48D PHE 3.3 0.2 - - - -
49D VAL* 3.5 16.8 + - - +
50D GLU* 3.4 22.0 + - - +
83D GLU* 3.5 19.0 + - - +
84D ILE* 4.3 11.8 - - + +
87D PHE* 3.4 56.2 - - + +
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Residues in contact with ALA 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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5D VAL* 4.8 1.1 - - + -
6D ARG* 3.8 36.0 - - + +
9D LEU* 4.0 14.7 - - + +
43D GLU 3.6 13.8 + - - +
44D ALA* 3.5 9.1 + - - +
45D LEU 3.3 0.6 - - - -
46D LYS* 1.3 77.7 - - - +
48D PHE* 1.3 62.7 + - - +
49D VAL 3.3 0.2 - - - -
50D GLU* 3.5 11.5 + - - +
51D ALA* 3.3 22.0 + - - +
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Residues in contact with PHE 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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9D LEU* 3.7 29.3 - - + +
26D TYR* 4.0 13.9 - + - -
29D ILE* 5.2 1.1 - - + -
30D LEU* 3.8 53.4 - - + -
44D ALA 3.7 7.1 + - - +
45D LEU 3.4 11.7 + - - +
46D LYS 3.3 0.6 - - - -
47D ALA* 1.3 77.9 - - - +
49D VAL* 1.3 65.1 + - + +
51D ALA* 3.5 4.3 + - - +
52D MET* 3.3 34.0 + - + +
65D LEU* 3.7 50.0 - - + -
66D LEU* 5.4 3.8 - - + -
69D PHE* 5.3 11.2 - + + -
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Residues in contact with VAL 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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45D LEU 3.9 13.9 - - - +
46D LYS* 3.5 10.7 + - - +
47D ALA 3.3 0.6 - - - -
48D PHE* 1.3 76.2 - - + +
50D GLU* 1.3 64.9 + - + +
52D MET* 3.3 13.7 + - - +
53D VAL* 3.3 18.8 + - + +
66D LEU* 5.7 6.5 - - + -
69D PHE* 4.6 14.6 - - + -
84D ILE* 5.7 1.6 - - + -
87D PHE* 5.1 7.4 - - + +
88D THR* 3.7 44.2 - - + +
91D LYS* 3.9 25.4 - - + -
92D ILE* 4.9 3.1 - - + -
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Residues in contact with GLU 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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6D ARG* 4.3 17.3 + - - -
13D MET* 5.4 0.4 - - - -
46D LYS* 3.4 20.7 + - - +
47D ALA* 3.5 11.5 + - - +
49D VAL* 1.3 77.7 - - + +
51D ALA* 1.3 51.6 + - - +
52D MET 3.3 0.2 - - - -
53D VAL* 3.4 14.2 - - - +
54D ASN* 2.5 33.5 + - - +
87D PHE* 4.7 15.0 - - + -
91D LYS* 3.7 29.9 + - + +
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Residues in contact with ALA 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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9D LEU* 4.4 18.2 - - + +
13D MET* 3.6 22.6 - - + +
26D TYR* 5.2 0.4 - - - +
47D ALA 3.3 16.7 + - - +
48D PHE* 3.9 8.5 - - - +
49D VAL 3.2 0.8 - - - -
50D GLU* 1.3 78.5 - - - +
52D MET* 1.3 69.9 + - + +
54D ASN* 3.5 10.2 + - - +
57D VAL* 3.3 26.3 - - - +
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Residues in contact with MET 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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26D TYR* 3.7 32.5 - - + +
48D PHE* 3.3 33.0 - - + +
49D VAL* 3.3 7.4 + - - +
51D ALA* 1.3 103.9 - - + +
53D VAL* 1.3 61.9 + - + +
54D ASN 3.2 9.2 + - - +
57D VAL* 4.4 6.6 - - + +
62D SER* 3.2 44.5 + - - +
65D LEU* 3.7 26.2 - - + -
66D LEU* 4.5 21.8 - - + -
95D ARG* 4.0 4.9 + - - -
99D PHE* 4.0 6.1 - - - -
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Residues in contact with VAL 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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49D VAL* 3.3 16.2 - - + +
50D GLU 3.4 17.0 - - - +
52D MET* 1.3 75.8 - - + +
54D ASN* 1.3 61.8 + - - +
55D GLU* 4.0 1.2 + - - +
66D LEU* 6.6 0.4 - - + -
91D LYS* 3.6 52.3 - - + +
92D ILE* 4.1 22.4 - - + -
95D ARG* 2.7 35.4 + - + +
99D PHE* 4.9 4.5 - - + -
538O GLN* 5.5 1.4 + - - -
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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