Contacts of the helix formed by residues 39 - 58 (chain B) in PDB entry 4I7Z
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 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A CYS* 6.2 2.0 - - - -
34B ASN 3.3 20.0 - - - +
35B ASP* 3.0 24.2 + - - +
38B TYR* 1.3 83.0 - - + +
40B PHE* 1.3 68.6 + - + +
41B PRO 3.3 1.6 - - - -
42B VAL* 3.1 19.0 + - + +
43B VAL* 3.2 20.2 + - + +
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Residues in contact with PHE 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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35A CYS* 6.4 2.7 - - - -
35B ASP* 3.0 51.3 + - + -
36B LEU* 3.5 35.4 - - + +
39B VAL* 1.3 79.8 - - + +
41B PRO* 1.3 68.9 - - + +
43B VAL* 3.0 13.1 + - + +
44B ILE* 2.9 33.0 + - + +
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Residues in contact with PRO 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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36B LEU 3.4 11.4 - - - +
37B LEU* 3.4 19.7 - - + +
38B TYR 4.6 2.2 - - - +
39B VAL 3.5 9.2 - - - +
40B PHE* 1.3 95.3 - - + +
42B VAL* 1.3 56.5 + - + +
44B ILE* 3.3 12.2 + - + -
45B MET* 2.8 48.2 + - + +
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Residues in contact with VAL 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 TYR 3.3 24.0 - - - +
39B VAL* 3.1 12.7 + - + +
41B PRO* 1.3 76.1 - - + +
43B VAL* 1.3 60.1 + - + +
45B MET* 3.8 7.5 - - - +
46B GLY* 2.8 28.4 + - - -
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Residues in contact with VAL 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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35A CYS* 4.5 21.3 - - + -
38A GLY 5.8 0.9 - - - -
39A ILE* 3.5 38.1 - - + -
42A THR* 5.7 1.3 - - - +
39B VAL* 3.4 22.9 - - + +
40B PHE* 3.0 10.7 + - + +
42B VAL* 1.3 75.7 - - + +
44B ILE* 1.3 57.2 + - + +
46B GLY* 3.3 1.0 + - - -
47B THR* 2.8 40.0 + - - +
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Residues in contact with ILE 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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42A THR* 4.0 34.6 - - + +
40B PHE* 2.9 28.6 + - + +
41B PRO* 3.6 11.0 - - + +
43B VAL* 1.3 76.6 - - + +
45B MET* 1.3 63.7 + - + +
47B THR* 3.2 4.7 + - - -
48B PHE* 2.9 30.7 + - + +
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Residues in contact with MET 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 PRO* 2.8 35.8 + - + +
42B VAL* 4.0 6.1 - - - +
44B ILE* 1.3 75.5 - - + +
46B GLY* 1.3 57.6 + - - +
48B PHE* 3.9 7.5 - - - +
49B ALA* 2.8 33.4 + - - +
261C PHE* 5.8 0.2 - - - -
264C LEU* 5.4 9.6 - - + +
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Residues in contact with GLY 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 VAL 2.8 19.6 + - - -
43B VAL* 3.7 1.1 - - - -
45B MET* 1.3 75.3 - - - +
47B THR* 1.3 61.5 + - - +
49B ALA* 3.2 5.6 + - - +
50B CYS* 2.9 33.4 + - - -
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Residues in contact with THR 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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39A ILE* 3.7 25.8 - - + +
42A THR* 4.2 17.2 - - + +
43A CYS* 4.1 16.8 - - - -
46A ILE* 4.9 0.4 - - + -
43B VAL* 2.8 23.9 + - - +
44B ILE* 3.5 7.5 - - - -
46B GLY* 1.3 76.7 - - - +
48B PHE* 1.3 63.3 + - - +
50B CYS* 3.2 5.4 + - - +
51B ILE* 2.9 47.7 + - + +
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Residues in contact with PHE 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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42A THR* 5.9 0.4 - - + -
46A ILE* 3.9 36.1 - - + +
85A ILE* 4.5 14.6 - - + -
44B ILE* 2.9 20.8 + - + +
45B MET* 3.9 7.0 - - - +
47B THR* 1.3 76.2 - - - +
49B ALA* 1.3 57.5 + - - +
51B ILE* 3.3 3.0 + - + +
52B VAL* 2.8 58.0 + - + +
261C PHE* 3.7 31.2 - + - -
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Residues in contact with ALA 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 MET 2.8 23.5 + - - +
46B GLY* 3.5 6.5 - - - +
48B PHE* 1.3 74.2 - - - +
50B CYS* 1.3 58.6 + - - +
52B VAL* 3.3 5.7 + - - +
53B ALA* 2.9 31.1 + - - +
261C PHE* 4.5 13.7 - - + -
262C ILE* 4.0 24.4 - - + +
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Residues in contact with CYS 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 GLY* 2.9 22.3 + - - +
47B THR* 3.7 5.4 - - - +
49B ALA* 1.3 75.4 - - - +
51B ILE* 1.3 59.6 + - + +
53B ALA* 3.3 5.8 + - - +
54B LEU* 2.9 41.1 + - + +
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Residues in contact with ILE 51 (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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43A CYS* 4.1 9.0 - - - -
46A ILE* 3.7 19.3 - - + -
85A ILE* 4.1 17.9 - - + +
88A TRP* 4.2 2.7 - - + -
89A SER* 3.6 41.3 - - - +
92A MET* 4.4 17.5 - - + -
47B THR* 2.9 34.7 + - + +
48B PHE* 3.7 4.9 - - + +
50B CYS* 1.3 77.2 - - + +
52B VAL* 1.3 54.8 + - + +
54B LEU* 3.4 8.9 + - + +
55B SER* 2.6 44.8 + - - +
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Residues in contact with VAL 52 (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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81A LEU* 4.9 9.2 - - + -
85A ILE* 4.0 13.5 - - + -
48B PHE* 2.8 60.2 + - + +
49B ALA* 3.6 5.4 - - - +
51B ILE* 1.3 69.7 - - + +
53B ALA* 1.3 63.4 + - - +
55B SER* 3.1 7.1 + - - -
56B VAL* 2.8 36.2 + - + +
258C MET* 4.3 16.8 - - + -
261C PHE* 4.5 16.2 - - + -
262C ILE* 5.0 0.4 - - + -
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Residues in contact with ALA 53 (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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49B ALA 2.9 17.8 + - - +
50B CYS* 3.6 7.4 - - - +
52B VAL* 1.3 77.9 - - - +
54B LEU* 1.3 57.8 + - + +
56B VAL* 3.2 1.0 + - - +
57B LEU* 2.9 41.9 + - + +
258C MET* 3.8 30.3 - - + +
262C ILE* 4.4 5.8 - - + -
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Residues in contact with LEU 54 (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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88A TRP* 3.2 57.2 + - + -
92A MET* 4.9 15.9 - - + -
50B CYS* 2.9 28.0 + - + +
51B ILE* 3.6 8.1 - - - +
53B ALA* 1.3 75.6 - - + +
55B SER* 1.3 54.8 + - - +
57B LEU* 4.9 5.8 - - + -
58B ASP* 2.8 33.1 + - + +
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Residues in contact with SER 55 (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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80A TRP* 4.6 3.4 - - - -
81A LEU* 4.1 6.1 - - - -
84A SER* 3.4 23.2 + - - -
85A ILE* 3.2 35.8 + - - +
88A TRP* 3.6 12.0 - - - -
51B ILE* 2.6 28.5 + - - +
52B VAL 3.4 4.9 - - - -
54B LEU* 1.3 72.9 - - - +
56B VAL* 1.3 62.8 + - - +
59B PRO* 3.2 25.6 - - - +
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Residues in contact with VAL 56 (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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80A TRP* 4.4 22.6 - - + -
81A LEU* 4.7 7.9 - - + -
52B VAL* 2.8 27.0 + - + +
53B ALA 3.8 3.1 - - - +
55B SER* 1.3 79.4 - - - +
57B LEU* 1.3 66.9 + - + +
59B PRO* 3.5 8.1 - - - +
250C GLN* 3.2 20.8 + - - +
254C ARG* 3.7 37.4 + - + +
255C VAL* 4.3 6.3 - - - +
258C MET* 3.9 29.4 - - + -
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Residues in contact with LEU 57 (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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53B ALA* 2.9 26.0 + - + +
54B LEU* 4.4 5.8 - - + +
56B VAL* 1.3 79.3 - - + +
58B ASP* 1.3 60.8 + - + +
59B PRO* 3.5 6.0 - - - +
38C GLN* 3.5 22.0 + - - +
39C SER* 4.2 3.6 + - - -
248C VAL* 4.2 0.9 - - - +
250C GLN* 3.9 11.5 + - - +
255C VAL* 4.4 20.2 - - + -
258C MET* 3.7 26.7 - - + -
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Residues in contact with ASP 58 (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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88A TRP* 2.8 42.9 + - + -
54B LEU* 2.8 18.3 + - + +
57B LEU* 1.3 80.6 - - + +
59B PRO* 1.3 67.8 - - - +
38C GLN* 4.4 15.1 + - - +
146C LYS* 2.9 33.4 + - - +
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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