Contacts of the helix formed by residues 40 - 57 (chain D) in PDB entry 3H2U
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 ASP 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D LEU* 1.3 82.1 - - - +
41D PRO* 1.4 85.4 - - - +
42D GLU* 2.9 23.6 + - - +
43D GLU* 3.8 15.8 + - + -
44D ILE* 2.9 23.4 + - - +
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Residues in contact with PRO 41 (chain D).
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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39D LEU 4.7 0.7 - - - +
40D ASP* 1.4 101.8 - - - +
42D GLU* 1.3 64.5 + - + +
43D GLU 3.3 1.1 - - - -
44D ILE* 3.9 11.5 - - + +
45D ARG* 3.4 24.4 + - - +
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Residues in contact with GLU 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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40D ASP* 2.9 12.4 + - - +
41D PRO* 1.3 87.9 - - + +
43D GLU* 1.3 61.6 + - - +
45D ARG* 2.8 41.4 + - - +
46D LYS* 3.1 27.9 + - - +
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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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39D LEU* 4.4 15.9 - - + -
40D ASP* 3.8 21.4 + - + +
42D GLU* 1.3 79.8 - - - +
44D ILE* 1.3 65.6 + - - +
46D LYS* 3.0 25.8 + - - +
47D ARG* 2.8 65.2 + - - +
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Residues in contact with ILE 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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39D LEU* 3.0 26.0 - - + +
40D ASP 2.9 25.1 + - - +
41D PRO* 4.0 10.3 - - + +
43D GLU* 1.3 78.5 - - - +
45D ARG* 1.3 58.9 + - + +
47D ARG* 3.3 3.5 + - - +
48D LEU* 3.0 35.7 + - + +
167D GLU 3.8 19.7 - - - +
168D ARG 2.9 15.7 - - - +
169D THR* 2.8 22.4 - - - +
170D GLY* 4.1 9.6 - - - -
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Residues in contact with ARG 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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41D PRO 3.4 17.3 + - - +
42D GLU* 2.8 55.3 + - - +
44D ILE* 1.3 81.3 - - + +
46D LYS* 1.3 69.0 + - - +
48D LEU* 4.1 6.8 - - - +
49D GLU* 2.8 70.0 + - - +
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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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42D GLU 3.1 20.9 + - - +
43D GLU* 3.0 32.8 + - - +
45D ARG* 1.3 90.6 - - - +
47D ARG* 1.3 62.6 + - + +
49D GLU* 3.3 7.6 - - - +
50D HIS* 3.0 28.9 + - + +
53D ARG* 5.3 0.9 + - - -
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Residues in contact with ARG 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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39D LEU* 4.8 10.7 - - - +
43D GLU* 2.8 54.5 + - - +
44D ILE* 3.6 5.2 - - - +
46D LYS* 1.3 75.8 - - + +
48D LEU* 1.3 63.9 + - + +
49D GLU 2.9 5.5 + - - -
50D HIS* 3.1 7.3 + - - +
51D THR* 3.0 23.6 + - - -
144D THR* 5.7 7.5 - - - +
165D TYR* 3.5 46.7 - - + +
170D GLY 2.5 39.4 + - - +
171D GLN* 3.8 15.0 + - - +
172D SER* 4.0 3.0 - - - +
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Residues in contact with LEU 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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44D ILE* 3.0 22.1 + - + +
45D ARG* 4.1 6.1 - - - +
47D ARG* 1.3 78.7 - - + +
49D GLU* 1.3 60.7 + - - +
51D THR* 3.7 7.5 + - + +
52D GLU* 3.2 28.9 + - + +
165D TYR* 4.0 28.9 - - + +
166D SER 4.0 13.9 - - - +
167D GLU* 3.1 51.1 - - - +
170D GLY* 5.4 0.7 - - - -
219D HIS* 6.0 0.2 - - + -
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Residues in contact with GLU 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 ARG* 2.8 59.4 + - - +
46D LYS* 3.3 8.6 - - - +
47D ARG 2.9 0.4 - - - -
48D LEU* 1.3 75.9 - - - +
50D HIS* 1.3 65.2 - - - +
52D GLU* 3.2 7.9 + - - +
53D ARG* 3.2 44.5 + - + +
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Residues in contact with HIS 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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46D LYS* 3.0 13.1 + - + +
47D ARG* 3.7 8.1 - - - +
49D GLU* 1.3 78.8 - - - +
51D THR* 1.3 63.7 + - - +
53D ARG* 3.5 32.6 + - + +
54D GLN* 3.1 47.4 + - + +
145D GLN* 4.1 34.5 + - + +
161D CYS 4.7 0.2 - - - -
165D TYR* 5.9 2.2 - - - +
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Residues in contact with THR 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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47D ARG 3.0 12.1 + - - -
48D LEU* 4.0 8.1 - - + +
50D HIS* 1.3 77.1 + - - +
52D GLU* 1.3 55.8 + - + +
54D GLN* 3.1 3.6 + - - +
55D PHE* 2.8 33.1 + - + +
145D GLN* 4.6 2.4 + - - -
162D PHE* 3.8 25.3 - - + +
163D LEU 2.8 29.6 + - - +
164D VAL* 5.0 5.8 - - + -
165D TYR* 3.3 19.9 - - + +
218D LEU* 4.9 9.0 - - + -
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Residues in contact with GLU 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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48D LEU 3.2 17.9 + - - +
49D GLU* 3.2 10.3 + - - +
51D THR* 1.3 76.0 - - + +
53D ARG* 1.3 66.1 + - - +
55D PHE* 3.2 9.6 + - - +
56D ARG* 2.8 65.0 + - + +
215D PRO* 3.8 24.4 - - - +
218D LEU* 5.6 1.7 - - - +
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Residues in contact with ARG 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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46D LYS 5.3 0.8 + - - -
49D GLU* 3.2 39.6 + - + +
50D HIS* 3.6 41.3 - - + +
52D GLU* 1.3 79.0 - - + +
54D GLN* 1.3 59.3 + - + +
56D ARG* 3.9 3.1 - - - +
57D ASN* 3.1 30.1 + - - +
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Residues in contact with GLN 54 (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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50D HIS* 3.1 32.8 + - + +
51D THR 3.1 8.9 + - - +
52D GLU 3.1 0.4 - - - -
53D ARG* 1.3 80.4 - - - +
55D PHE* 1.3 66.9 + - - +
57D ASN* 3.1 11.9 + - - +
159D GLU 4.5 2.6 + - - -
160D ARG* 3.0 36.8 - - - +
161D CYS* 2.6 47.2 + - - +
162D PHE* 3.6 16.4 - - + -
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Residues in contact with PHE 55 (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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51D THR* 2.8 20.1 + - + +
52D GLU* 3.7 16.4 - - - +
54D GLN* 1.3 73.8 - - - +
56D ARG* 1.3 82.5 + - + +
58D ARG* 3.8 5.2 - - - +
160D ARG* 2.8 38.4 + - - -
162D PHE* 3.8 21.2 - + + -
213D LEU* 2.4 41.3 - - + -
214D THR* 3.8 4.7 - - - -
215D PRO* 3.5 25.6 - - + -
218D LEU* 3.7 28.7 - - + -
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Residues in contact with ARG 56 (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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52D GLU* 2.8 46.1 + - - +
53D ARG* 3.9 3.1 - - - +
55D PHE* 1.3 87.1 - - + +
57D ASN* 1.3 49.7 + - - +
58D ARG* 2.6 25.5 + - - +
103D GLY* 4.3 8.5 - - - -
215D PRO* 3.5 35.1 - - - +
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Residues in contact with ASN 57 (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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53D ARG 3.1 16.3 + - - +
54D GLN* 3.1 15.4 + - - +
56D ARG* 1.3 73.0 - - - +
58D ARG* 1.3 60.2 + - - +
59D ARG* 3.4 25.9 + - - +
101D LEU 4.9 0.8 + - - -
102D ASN* 3.4 12.0 - - - +
103D GLY* 3.1 22.6 + - - +
104D GLU* 4.7 2.9 - - - +
159D GLU* 4.2 16.0 + - - +
160D ARG* 3.7 18.1 - - + +
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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