Contacts of the helix formed by residues 41 - 62 (chain D) in PDB entry 5H15
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 MET 41 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B LEU* 4.0 27.6 - - + -
332B LYS* 3.7 18.4 - - + -
336B MET* 3.1 44.6 - - + +
353B LEU* 4.3 19.1 - - + -
40D SER* 1.3 72.9 - - - +
42D PHE* 1.3 58.8 + - + +
44D SER* 3.9 4.8 - - - -
45D ASN* 3.1 29.6 + - - +
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Residues in contact with PHE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 6.0 1.8 - - - -
391B LEU 3.6 17.5 - - - -
392B GLU* 3.3 30.1 - - - -
393B VAL 4.1 1.1 - - - -
394B GLU* 3.4 65.0 + - + +
40D SER* 3.3 3.7 + - - +
41D MET* 1.3 76.8 - - - +
43D SER* 1.4 61.5 + - - +
45D ASN* 3.0 8.0 + - - +
46D ARG* 2.8 55.3 + - + +
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Residues in contact with SER 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D SER* 3.1 29.4 + - - -
42D PHE* 1.4 83.8 - - - +
44D SER* 1.3 59.0 + - - +
46D ARG* 3.3 9.9 + - - +
47D GLN* 2.9 30.9 + - - +
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Residues in contact with SER 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D SER 3.1 18.5 + - - -
41D MET* 3.9 5.2 - - - -
43D SER* 1.3 80.9 + - - +
45D ASN* 1.4 60.4 + - - +
47D GLN* 3.5 8.5 + - - +
48D LYS* 3.2 39.6 + - - +
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Residues in contact with ASN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 2.8 22.3 + - - +
316B GLY* 3.6 2.0 - - - -
317B ASP* 2.9 39.0 - - - +
318B LEU* 3.5 26.7 - - + +
41D MET* 3.1 19.2 + - - +
42D PHE* 3.0 5.4 + - - +
44D SER* 1.4 72.8 - - - +
46D ARG* 1.4 58.6 + - - +
48D LYS* 3.3 11.8 + - - +
49D ILE* 3.1 45.1 + - - +
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Residues in contact with ARG 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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315B LEU* 3.8 8.1 - - - +
373B TRP 4.1 7.9 + - - -
374B GLN 2.6 32.9 + - - -
375B LYS* 4.3 5.5 - - - +
391B LEU* 3.5 30.8 + - - +
392B GLU* 4.2 23.4 + - - +
42D PHE* 2.8 43.6 + - + +
43D SER* 3.4 12.8 - - - +
45D ASN* 1.4 69.6 - - - +
47D GLN* 1.4 58.2 + - - +
49D ILE* 3.4 35.4 + - - +
50D LEU* 3.0 28.8 + - - +
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Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D SER 2.9 16.8 + - - +
44D SER* 3.5 9.9 - - - +
45D ASN 3.3 0.2 - - - -
46D ARG* 1.4 76.4 - - - +
48D LYS* 1.4 57.2 + - + +
50D LEU* 3.2 23.4 + - - +
51D GLU* 3.0 58.3 + - - +
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Residues in contact with LYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 5.1 0.2 - - - -
316B GLY* 5.2 1.3 - - - -
317B ASP* 2.8 36.6 + - - +
339B ASP* 6.3 1.2 - - - -
44D SER* 3.2 26.9 + - - +
45D ASN* 3.3 17.0 + - - +
47D GLN* 1.4 74.1 - - + +
49D ILE* 1.3 60.2 + - - +
51D GLU* 3.9 11.1 - - - +
52D ARG* 2.9 69.2 + - - +
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 3.9 7.0 - - + -
315B LEU* 3.7 17.0 - - + -
316B GLY* 3.6 20.4 - - - +
373B TRP 3.6 22.9 - - - +
374B GLN* 3.6 19.7 - - + +
45D ASN* 3.1 35.6 + - - +
46D ARG* 3.6 39.7 - - - +
47D GLN 3.3 0.2 - - - -
48D LYS* 1.3 72.0 - - - +
50D LEU* 1.4 52.0 + - - +
53D THR* 2.7 46.6 + - + +
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TRP* 5.0 14.6 - - + -
375B LYS* 6.1 5.8 - - - +
46D ARG 3.0 14.9 + - - +
47D GLN* 3.4 30.7 - - - +
49D ILE* 1.4 74.8 - - - +
51D GLU* 1.3 58.9 + - + +
53D THR* 3.3 6.5 + - - +
54D GLU* 3.1 32.8 + - + +
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Residues in contact with GLU 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 GLN* 3.0 43.7 + - - +
48D LYS* 4.0 12.9 - - - +
50D LEU* 1.3 78.4 - - + +
52D ARG* 1.4 62.8 + - + +
54D GLU* 3.4 8.2 + - - +
55D ILE* 3.2 31.8 + - + +
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Residues in contact with ARG 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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245B ASP* 5.6 2.0 + - - -
246B LEU* 3.8 27.8 - - + +
247B LEU* 3.7 36.8 - - + +
250B LYS* 5.6 4.0 - - - +
316B GLY* 4.4 10.1 + - - -
317B ASP* 2.9 27.5 + - - -
48D LYS* 2.9 56.4 + - - +
51D GLU* 1.4 77.7 + - + +
53D THR* 1.3 65.4 + - - +
54D GLU 3.2 0.2 - - - -
55D ILE* 3.3 12.4 + - + +
56D LEU* 3.3 26.2 + - - +
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Residues in contact with THR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 3.7 28.7 - - + -
372B PHE* 3.4 29.9 - - + +
373B TRP* 3.2 31.0 + - - +
374B GLN* 4.7 0.9 - - - +
49D ILE* 2.7 42.3 + - + +
50D LEU* 3.3 7.8 + - - -
52D ARG* 1.3 70.6 - - - +
54D GLU* 1.4 51.5 + - - +
56D LEU* 3.4 4.1 + - - -
57D ASN* 2.8 34.8 + - - +
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Residues in contact with GLU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TRP* 3.9 20.5 - - + -
50D LEU* 3.1 24.6 + - + +
51D GLU* 3.6 7.9 - - - +
52D ARG 3.2 0.2 - - - -
53D THR* 1.4 73.7 + - - +
55D ILE* 1.4 58.9 + - + +
57D ASN* 4.3 4.8 + - - +
58D GLN* 2.9 64.3 + - + +
61D LYS* 5.6 0.9 + - - -
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Residues in contact with ILE 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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201B ARG* 4.0 20.2 - - - +
247B LEU* 4.0 25.4 - - + -
51D GLU* 3.2 19.0 + - + +
52D ARG* 3.3 10.5 + - + +
54D GLU* 1.4 75.6 - - + +
56D LEU* 1.3 59.6 + - - +
58D GLN* 3.4 6.1 + - - +
59D GLU* 3.0 49.7 + - + +
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Residues in contact with LEU 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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200B PRO* 3.6 24.2 - - + +
201B ARG* 3.6 26.7 - - - -
246B LEU* 3.4 48.7 - - + +
247B LEU* 5.2 2.0 - - + -
372B PHE* 4.0 20.9 - - + -
420B ARG* 4.3 0.6 + - - -
52D ARG 3.3 12.2 + - - +
53D THR* 3.7 7.2 - - - +
55D ILE* 1.3 75.3 - - - +
57D ASN* 1.3 60.3 + - - +
59D GLU* 3.3 9.3 + - - +
60D TRP* 3.0 28.6 + - - +
63D ARG* 5.2 1.2 + - - -
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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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372B PHE* 3.7 6.7 - - + -
373B TRP* 3.6 32.6 + - + -
420B ARG* 2.9 30.0 + - - +
53D THR 2.8 22.1 + - - +
54D GLU* 3.9 9.3 + - - +
55D ILE 3.3 0.2 - - - -
56D LEU* 1.3 73.2 - - - +
58D GLN* 1.4 57.0 + - - +
60D TRP* 3.3 15.8 + - - +
61D LYS* 2.9 57.8 + - - +
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Residues in contact with GLN 58 (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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54D GLU* 2.9 45.7 + - + +
55D ILE* 3.7 6.7 - - - +
57D ASN* 1.4 75.0 - - - +
59D GLU* 1.3 63.3 + - + +
61D LYS* 3.3 40.1 + - - +
62D GLN* 3.2 43.6 + - + +
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Residues in contact with GLU 59 (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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200B PRO 4.8 0.9 - - - +
201B ARG* 3.0 54.0 + - - +
55D ILE* 3.0 24.1 + - + +
56D LEU* 3.7 13.1 - - - +
58D GLN* 1.3 76.2 - - + +
60D TRP* 1.4 62.6 + - - +
62D GLN* 3.4 17.3 + - - +
63D ARG* 3.6 27.3 + - - +
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Residues in contact with TRP 60 (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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103B TRP 3.5 10.7 + - - -
104B HIS* 3.7 12.2 + - - -
105B SER 3.2 22.1 + - - -
106B LYS* 4.0 5.0 - - + +
107B GLU* 3.5 50.3 - - + -
420B ARG* 3.4 41.5 - - - +
56D LEU 3.0 14.8 + - - +
57D ASN* 3.3 30.5 + - - +
59D GLU* 1.4 74.4 - - - +
61D LYS* 1.3 88.6 + - + +
63D ARG* 3.2 42.1 + - - +
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Residues in contact with LYS 61 (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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54D GLU* 5.6 0.8 + - - -
57D ASN* 2.9 33.4 + - - +
58D GLN* 3.3 37.7 + - - +
60D TRP* 1.3 94.7 - - + +
62D GLN* 1.3 58.2 + - - +
63D ARG 3.2 4.0 + - - +
64D ARG* 2.8 30.7 + - - -
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Residues in contact with GLN 62 (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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275A LYS* 4.6 18.1 + - - -
58D GLN* 3.2 33.4 + - + +
59D GLU* 3.7 11.0 - - - +
60D TRP 3.3 0.6 - - - -
61D LYS* 1.3 80.3 - - - +
63D ARG* 1.3 59.0 + - + +
64D ARG* 3.6 12.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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