Contacts of the helix formed by residues 38 - 54 (chain A) in PDB entry 1ZHH
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 PHE 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A TRP* 4.2 16.2 - + - -
34A PHE* 3.0 50.6 + + - +
35A LEU 3.3 8.7 - - - +
37A GLU* 1.3 104.9 - - + +
39A PRO* 1.3 64.0 - - - +
40A GLU 3.2 2.2 - - - -
41A GLN* 2.9 42.2 + - + +
168A ASP* 5.7 4.5 - - - -
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Residues in contact with PRO 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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35A LEU 3.7 9.2 - - - +
36A ASP* 3.9 9.0 - - - +
37A GLU 3.5 9.4 - - - +
38A PHE* 1.3 85.5 - - - +
40A GLU* 1.3 61.3 + - - +
42A ARG* 3.1 15.3 + - + +
43A ASN* 3.4 15.4 + - - +
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Residues in contact with GLU 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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38A PHE* 3.2 1.6 - - + -
39A PRO* 1.3 77.0 - - - +
41A GLN* 1.3 67.0 + - - +
43A ASN* 3.1 27.3 + - - +
44A LEU* 3.0 47.2 + - + +
331A PRO* 5.8 0.9 - - - +
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Residues in contact with GLN 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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34A PHE* 3.8 22.3 - - + -
35A LEU* 3.8 9.2 - - + -
38A PHE* 2.9 33.6 + - + +
40A GLU* 1.3 79.9 - - + +
42A ARG* 1.3 54.5 + - - +
44A LEU* 3.4 18.1 + - - +
45A THR* 2.9 34.3 + - - -
332A VAL 4.9 2.4 + - - -
333A PRO* 3.5 7.1 - - - +
334A THR* 2.9 43.2 + - - +
335A VAL 4.7 0.2 + - - -
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Residues in contact with ARG 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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32A GLN* 2.8 36.0 + - - +
35A LEU* 3.5 48.9 + - + +
36A ASP* 2.9 29.5 + - - -
38A PHE 3.5 2.0 + - - -
39A PRO* 3.1 12.5 + - + +
41A GLN* 1.3 77.9 - - - +
43A ASN* 1.3 61.0 + - - +
45A THR* 3.8 1.1 - - - -
46A ASN* 2.9 56.7 + - - +
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Residues in contact with ASN 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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39A PRO* 3.4 10.6 + - - +
40A GLU* 3.1 34.9 + - - +
42A ARG* 1.3 79.5 - - - +
44A LEU* 1.3 58.6 + - - +
46A ASN* 3.5 9.4 + - - +
47A ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 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 GLU* 3.0 37.8 + - + +
41A GLN* 3.7 25.8 - - - +
43A ASN* 1.3 72.2 - - - +
45A THR* 1.3 60.8 + - - +
47A ALA* 3.3 8.0 + - + +
48A LEU* 3.0 27.5 + - - +
325A TRP* 4.0 4.6 - - + -
331A PRO* 3.8 43.1 - - + +
332A VAL 4.1 16.8 - - - +
333A PRO* 3.7 21.1 - - + +
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Residues in contact with THR 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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31A TYR* 3.3 26.5 - - - +
35A LEU* 3.6 21.1 - - + +
41A GLN* 2.9 20.6 + - - -
42A ARG* 3.8 3.8 - - - -
44A LEU* 1.3 76.7 - - - +
46A ASN* 1.3 60.0 + - - +
48A LEU* 3.2 4.1 + - - +
49A SER* 2.9 36.8 + - - +
333A PRO* 3.5 11.4 - - - +
335A VAL* 2.7 26.1 + - - +
336A TYR* 4.4 6.0 - - + -
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Residues in contact with ASN 46 (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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35A LEU* 5.9 0.7 - - - +
42A ARG* 2.9 44.6 + - - +
43A ASN* 3.8 9.9 + - - +
45A THR* 1.3 79.2 - - - +
47A ALA* 1.3 62.7 + - - +
49A SER* 3.3 8.3 + - - -
50A GLU* 3.0 36.2 + - - +
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Residues in contact with ALA 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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43A ASN 3.0 17.9 + - - +
44A LEU* 3.6 9.0 - - + +
45A THR 3.3 0.2 - - - -
46A ASN* 1.3 75.9 - - - +
48A LEU* 1.3 57.7 + - - +
50A GLU* 3.4 13.8 + - - +
51A ALA* 3.0 27.5 + - - +
325A TRP* 3.6 16.4 - - + -
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Residues in contact with LEU 48 (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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44A LEU 3.0 13.6 + - - +
45A THR 3.2 8.0 + - - +
47A ALA* 1.3 72.7 - - - +
49A SER* 1.3 67.0 + - - +
51A ALA* 3.2 1.0 + - + -
52A VAL* 2.9 35.3 + - + +
174A LEU* 4.6 8.3 - - + -
318A ALA* 4.0 16.6 - - + +
321A GLU* 3.6 31.4 - - + -
322A ALA* 4.4 6.7 - - + +
325A TRP* 3.5 21.7 - - + -
333A PRO* 3.7 22.7 - - + -
336A TYR* 3.9 30.7 - - + -
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Residues in contact with SER 49 (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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31A TYR* 5.3 0.5 + - - -
45A THR* 2.9 20.8 + - - +
46A ASN* 3.3 14.0 + - - -
48A LEU* 1.3 76.6 - - - +
50A GLU* 1.3 60.4 + - - +
52A VAL* 3.4 3.2 + - - +
53A ARG* 3.3 52.6 + - - +
336A TYR* 3.5 25.1 + - - -
337A SER 4.6 3.8 + - - -
339A ASP* 5.0 3.3 + - - +
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Residues in contact with GLU 50 (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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46A ASN* 3.0 26.4 + - - +
47A ALA* 3.7 11.5 - - - +
48A LEU 3.2 0.2 - - - -
49A SER* 1.3 75.0 - - - +
51A ALA* 1.3 62.5 + - - +
53A ARG* 3.4 21.4 + - - +
54A ALA* 3.2 24.3 + - - +
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Residues in contact with ALA 51 (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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47A ALA 3.0 17.6 + - - +
48A LEU* 3.2 4.9 + - + +
50A GLU* 1.3 76.5 - - - +
52A VAL* 1.3 59.3 + - - +
54A ALA* 3.4 13.4 + - - +
55A GLN 4.8 0.9 - - - +
92A ARG* 2.9 22.6 + - - -
321A GLU* 4.2 19.0 - - + +
324A LYS* 5.7 1.6 - - - +
325A TRP* 4.2 18.8 - - + +
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Residues in contact with VAL 52 (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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48A LEU* 2.9 25.3 + - + +
49A SER 3.6 6.3 - - - +
50A GLU 3.3 0.2 - - - -
51A ALA* 1.3 79.4 - - - +
53A ARG* 1.3 62.9 + - + +
54A ALA 3.8 4.2 - - - +
92A ARG* 3.8 2.9 + - - -
314A ASP* 3.7 19.1 - - - +
317A ILE* 3.8 17.9 - - + +
318A ALA* 3.6 38.1 - - + +
321A GLU* 4.7 1.3 - - + -
336A TYR* 3.6 20.9 - - + +
339A ASP* 5.5 0.4 - - - +
361A ARG* 3.1 28.9 + - - +
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Residues in contact with ARG 53 (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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49A SER* 3.3 37.6 + - - +
50A GLU* 3.9 20.7 - - - +
51A ALA 3.3 0.4 - - - -
52A VAL* 1.3 79.1 - - + +
54A ALA* 1.3 62.9 + - - +
55A GLN* 5.1 3.6 + - - -
314A ASP* 5.7 0.4 - - - +
339A ASP* 2.9 43.2 + - - +
358A ARG* 4.9 9.1 - - - +
361A ARG* 4.4 11.9 + - - +
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Residues in contact with ALA 54 (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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50A GLU 3.2 15.0 + - - +
51A ALA* 3.4 6.9 + - - +
52A VAL 3.4 0.4 - - - +
53A ARG* 1.3 83.4 - - - +
55A GLN* 1.3 70.0 + - - +
57A VAL* 6.3 0.7 - - + -
92A ARG* 3.0 26.7 + - - -
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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