Contacts of the helix formed by residues 33 - 47 (chain A) in PDB entry 1ORZ
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 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLY* 3.4 4.9 - - - -
32A ALA* 1.3 87.9 - - - +
34A GLY* 1.3 67.5 + - - -
35A ALA 3.3 2.9 - - - -
36A GLY 3.8 2.2 - - - +
37A LEU* 3.1 16.7 + - - +
61A SER* 3.6 22.8 - - - -
63A THR* 4.0 5.6 - - - -
164A LEU* 5.8 0.4 - - - -
218A ALA* 4.8 4.2 + - - -
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLY* 1.3 71.0 - - - +
35A ALA* 1.3 60.9 + - - +
37A LEU* 5.1 2.2 - - - -
38A ARG* 3.3 18.5 + - - +
63A THR* 3.1 28.3 + - - +
163A LEU* 4.9 7.6 - - - -
164A LEU* 5.8 3.1 - - - -
167A LEU* 3.5 21.6 - - - +
425A LEU* 3.9 12.5 - - - +
426A VAL* 5.2 1.0 - - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLY 3.3 0.2 - - - -
34A GLY* 1.3 74.5 - - - +
36A GLY* 1.3 65.7 + - - +
38A ARG* 3.1 3.9 + - - +
39A ALA* 3.0 24.1 + - - +
218A ALA* 4.6 3.1 - - + -
403A CYS* 3.5 32.3 - - + +
404A GLY* 3.8 7.2 - - - +
425A LEU* 3.5 41.8 - - + +
429A GLY* 4.2 2.6 - - - -
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.5 17.6 - - - +
31A GLY 3.0 26.5 - - - -
33A GLY 3.3 6.2 + - - -
35A ALA* 1.3 79.7 - - - +
37A LEU* 1.3 58.0 + - - +
39A ALA* 3.8 1.7 - - - +
40A ALA* 3.0 27.4 + - - +
52A CYS* 4.7 0.6 - - - -
218A ALA* 4.0 11.5 - - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA* 3.0 35.9 - - - +
33A GLY 3.1 8.7 + - - +
34A GLY* 4.1 1.6 - - - +
36A GLY* 1.3 74.0 - - - +
38A ARG* 1.3 66.8 + - - +
40A ALA* 3.1 5.5 + - + +
41A PHE* 2.8 26.8 + - - +
52A CYS* 4.5 12.3 - - + -
58A PRO* 4.5 16.2 - - + -
164A LEU* 4.0 14.4 - - + +
167A LEU* 3.9 33.7 - - + +
168A TYR* 3.9 23.6 - - + +
171A ALA* 5.3 10.3 - - + -
176A THR* 6.4 0.9 - - + -
178A PHE* 5.5 1.8 - - + -
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLY 3.3 11.7 + - - +
35A ALA 3.1 8.6 + - - +
37A LEU* 1.3 79.4 - - - +
39A ALA* 1.3 61.2 + - - +
41A PHE* 3.3 31.4 - - - +
42A GLY* 3.1 17.4 + - - +
112A SER* 6.1 0.4 - - - -
115A GLU* 3.0 37.0 + - - -
116A LEU* 4.8 6.1 - - - +
119A TYR* 4.7 3.6 + - - -
167A LEU* 4.2 23.5 - - + +
170A GLN* 5.6 1.1 - - - -
425A LEU 4.5 1.3 - - - +
426A VAL* 3.6 40.9 + - - +
429A GLY 4.7 0.3 - - - +
430A ARG* 3.0 40.8 - - - +
433A ALA* 4.7 0.2 - - - +
434A HIS* 4.2 3.6 + - - -
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.8 8.3 - - + -
35A ALA 3.0 15.0 + - - +
36A GLY* 3.8 6.3 - - - +
38A ARG* 1.3 75.9 - - - +
40A ALA* 1.3 60.0 + - - +
42A GLY 3.0 1.2 + - - -
43A LEU* 2.8 32.9 + - - +
216A ILE* 4.3 22.2 - - + -
403A CYS* 5.8 0.4 - - + -
429A GLY* 3.5 24.8 + - - +
432A VAL* 5.4 0.2 - - + -
433A ALA* 3.6 7.4 - - + +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.3 14.8 - - + +
36A GLY 3.0 18.0 + - - +
37A LEU* 3.1 9.4 + - + +
39A ALA* 1.3 74.9 - - - +
41A PHE* 1.3 61.6 + - - +
43A LEU* 3.5 4.5 + - - +
44A ALA* 3.1 24.1 + - - +
50A THR* 4.1 8.9 - - + +
52A CYS* 4.4 20.0 - - + -
176A THR* 4.3 19.7 + - + +
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU 2.8 17.4 + - - +
38A ARG* 3.3 27.4 - - - +
40A ALA* 1.3 77.0 - - - +
42A GLY* 1.3 69.2 + - - +
44A ALA* 3.1 8.7 + - - +
45A GLU* 3.0 37.0 + - + +
119A TYR* 3.5 28.5 - + - -
167A LEU* 6.0 0.7 - - + -
170A GLN* 3.7 28.5 - - + +
171A ALA* 5.7 4.0 - - - +
174A HIS* 2.8 56.3 - + + -
176A THR* 5.9 2.5 - - - -
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Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.1 11.3 + - - -
39A ALA 3.0 3.8 + - - -
41A PHE* 1.3 86.4 - - - +
43A LEU* 1.3 63.7 + - - +
45A GLU* 3.1 16.8 + - - +
46A ALA* 3.2 11.3 + - - +
433A ALA* 3.5 23.5 - - - +
434A HIS* 6.1 2.5 - - - -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A CYS* 2.9 44.2 - - + -
29A VAL* 4.8 4.3 - - + -
39A ALA 2.8 16.8 + - - +
40A ALA 3.8 4.7 - - - +
42A GLY* 1.3 74.8 - - - +
44A ALA* 1.3 57.8 + - - +
46A ALA* 2.8 24.4 - - + +
47A GLY 3.5 2.4 + - - -
48A TYR* 3.1 40.8 - - + +
49A LYS 4.6 0.9 - - - +
50A THR* 3.3 18.2 - - + +
214A LYS* 6.2 0.2 - - - +
433A ALA* 3.4 11.3 - - + +
436A VAL* 4.4 17.7 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA 3.1 14.5 + - - +
41A PHE* 3.1 11.6 + - - +
43A LEU* 1.3 72.7 - - - +
45A GLU* 1.3 59.6 + - - +
46A ALA 3.0 2.0 - - - -
47A GLY* 2.8 21.5 + - - -
48A TYR 4.0 10.5 + - - -
50A THR* 4.8 4.0 - - + +
174A HIS* 5.0 18.6 - - + +
176A THR* 4.9 11.7 - - - +
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.0 27.0 + - + +
42A GLY* 3.1 13.4 + - - +
44A ALA* 1.3 75.8 - - - +
46A ALA* 1.3 61.3 + - - +
47A GLY* 3.2 1.7 + - - -
174A HIS* 3.4 30.6 + - - -
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLY 3.2 5.8 + - - +
43A LEU* 2.8 22.8 + - + +
44A ALA 3.0 0.2 - - - -
45A GLU* 1.3 80.0 - - - +
47A GLY* 1.3 56.7 + - - +
48A TYR* 3.3 30.5 - - + -
433A ALA 5.1 2.7 - - - +
436A VAL* 4.9 9.4 - - + -
437A ALA* 6.0 0.7 - - + -
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASP* 5.1 0.3 - - - +
44A ALA 2.8 13.7 + - - -
45A GLU 3.1 2.1 - - - -
46A ALA* 1.3 79.0 - - - +
48A TYR* 1.3 68.5 + - - +
49A LYS* 4.1 6.0 + - - +
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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