Contacts of the helix formed by residues 36 - 50 (chain B) in PDB entry 1H9D
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 PRO 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ASP 4.7 0.7 - - - +
35B ARG* 1.3 94.1 - - + +
37B HIS* 1.3 67.2 + - - +
38B GLU* 4.3 12.6 - - + +
39B GLU* 3.1 29.1 + - + +
40B ARG* 3.2 8.7 + - - +
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Residues in contact with HIS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG 3.6 1.6 + - - -
36B PRO* 1.3 72.2 - - - +
38B GLU* 1.3 78.5 + - - +
40B ARG* 3.0 18.3 + - - +
41B GLN* 3.0 36.6 + - - -
117B GLN* 2.8 35.6 + - - -
118B ARG* 3.8 12.3 - - - -
119B LEU* 3.8 23.7 - - + +
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 3.2 10.0 + - + +
37B HIS* 1.3 95.0 + - - +
39B GLU* 1.3 62.0 + - - +
41B GLN* 3.1 23.1 + - - +
42B ALA* 3.2 18.2 + - - +
90D ARG* 5.9 7.9 - - - +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 3.1 40.4 + - + +
36B PRO* 3.1 23.9 + - + +
38B GLU* 1.3 75.0 - - - +
40B ARG* 1.3 56.7 + - - +
41B GLN 3.0 1.6 - - - -
42B ALA* 2.7 12.6 + - + +
43B ARG* 2.7 72.3 + - + +
90D ARG 4.7 14.4 - - - +
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 5.5 1.4 + - - -
28B LYS* 6.2 0.2 - - - +
29B TYR* 3.0 46.2 + - + -
30B THR* 3.7 3.2 + - - +
31B GLY 2.7 29.9 + - - +
32B PHE* 3.1 22.2 + - + +
33B ARG* 3.8 17.3 - - - +
35B ARG* 3.6 15.0 - - + +
36B PRO 3.4 13.0 - - - +
37B HIS* 3.0 18.9 + - - +
39B GLU* 1.3 76.3 - - - +
41B GLN* 1.3 57.5 + - - +
43B ARG* 3.8 8.0 - - - +
44B PHE* 2.8 32.1 + - - +
119B LEU* 3.8 21.7 - - + +
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Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B HIS* 3.0 30.9 + - - +
38B GLU* 3.1 35.8 + - - +
40B ARG* 1.3 77.7 - - - +
42B ALA* 1.3 63.6 + - - +
44B PHE* 3.5 3.1 - - - +
45B GLN* 3.2 24.2 + - - +
116B LEU 3.6 19.6 - - - +
117B GLN* 3.1 32.7 + - - +
119B LEU* 3.9 13.9 - - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLU 3.2 7.2 + - - +
39B GLU* 2.7 18.1 + - + +
41B GLN* 1.3 72.7 - - - +
43B ARG* 1.3 64.3 + - + +
45B GLN* 3.0 7.3 + - - +
46B ASN* 2.7 34.7 + - - +
90D ARG 5.0 3.1 - - - +
91D GLU* 3.0 41.3 - - + +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 4.0 2.5 - - - +
32B PHE* 3.8 54.9 - - + -
35B ARG* 4.0 8.3 - - - +
39B GLU* 2.7 58.5 + - + +
40B ARG* 3.8 6.3 - - - +
42B ALA* 1.3 73.0 - - - +
44B PHE* 1.3 67.5 + - - +
46B ASN* 3.2 13.2 - - - +
47B ALA* 3.1 24.3 + - - +
92D ALA* 5.7 8.3 - - - +
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 3.3 39.6 + + + -
40B ARG 2.8 20.0 + - - +
41B GLN 3.5 4.0 - - - +
43B ARG* 1.3 77.7 - - - +
45B GLN* 1.3 63.1 + - + +
47B ALA* 3.4 3.4 + - - +
48B CYS* 2.9 49.7 + - - +
53B SER* 3.5 19.7 + - - -
55B ILE* 5.0 0.2 - - + -
95B VAL* 4.0 7.9 - - + -
97B LEU* 4.5 1.8 - - + -
114B ILE* 3.6 44.4 - - + -
116B LEU* 3.9 23.1 - - + -
119B LEU* 3.7 20.6 - - + -
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLN 3.2 10.8 + - - +
42B ALA* 3.0 9.2 + - - +
44B PHE* 1.3 77.4 - - + +
46B ASN* 1.3 67.4 + - - +
48B CYS* 3.1 8.1 + - + +
49B ARG* 2.9 46.1 + - + +
88B LEU* 4.6 14.1 - - + +
116B LEU* 3.6 48.5 + - + +
91D GLU* 5.8 0.2 - - - +
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Residues in contact with ASN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 2.7 45.9 + - - +
43B ARG* 3.1 19.1 - - - +
44B PHE 3.4 0.2 - - - -
45B GLN* 1.3 75.5 - - - +
47B ALA* 1.3 62.4 + - - +
49B ARG* 2.9 33.4 + - - +
50B ASP* 3.1 24.7 + - - +
91D GLU* 2.6 31.3 + - - +
92D ALA 5.0 5.1 + - - +
94D LYS* 5.1 0.2 - - - +
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 5.5 4.7 - - + +
32B PHE* 6.1 2.9 - - + -
43B ARG 3.1 15.1 + - - +
44B PHE* 3.7 3.6 - - - +
46B ASN* 1.3 75.6 - - - +
48B CYS* 1.3 62.5 + - - +
50B ASP* 2.8 31.7 + - - +
52B ARG* 2.9 51.7 + - - +
53B SER* 5.1 2.9 - - - -
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Residues in contact with CYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PHE* 2.9 52.0 + - + +
45B GLN* 3.1 12.8 + - + +
47B ALA* 1.3 75.2 - - - +
49B ARG* 1.3 57.2 + - + +
51B GLY* 2.6 26.0 + - - -
52B ARG 3.6 4.5 - - - +
53B SER* 4.3 10.5 - - - -
68B PHE* 4.4 1.8 - - - -
86B VAL* 3.5 24.5 - - + +
95B VAL* 4.7 5.2 - - + -
97B LEU* 4.1 20.0 - - - -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLN* 2.9 30.5 + - - +
46B ASN* 2.9 48.6 + - - +
48B CYS* 1.3 76.9 - - + +
50B ASP* 1.3 56.6 + - - +
51B GLY 3.1 0.2 - - - -
80B THR* 4.6 4.0 + - - +
81B PRO* 2.9 28.4 - - - +
86B VAL* 4.8 5.6 - - + -
88B LEU* 4.8 18.4 - - + -
91D GLU* 3.9 6.1 + - - -
94D LYS* 4.8 11.5 - - - +
115D ASP* 5.6 3.8 + - - -
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASN* 3.1 17.4 + - - +
47B ALA* 2.8 18.5 + - - +
49B ARG* 1.3 78.1 - - - +
51B GLY* 1.3 61.7 + - - +
52B ARG* 3.5 23.8 + - - +
69B PHE* 3.7 10.4 - - - -
81B PRO* 4.3 4.5 - - - -
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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