Contacts of the helix formed by residues 44 - 64 (chain A) in PDB entry 5N4D
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 THR 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A TRP* 5.5 0.2 - - - -
42A GLU* 4.0 9.7 + - + -
43A SER* 1.3 81.0 + - - +
45A ASP* 1.3 65.6 + - - +
46A GLU* 3.3 11.2 + - - +
47A VAL* 3.1 26.0 + - + +
48A ASP* 2.9 30.6 + - - -
42B GLU* 3.5 26.2 - - + -
44B THR* 3.4 31.2 - - + -
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Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 1.3 72.7 - - - +
46A GLU* 1.3 57.0 + - - +
48A ASP* 3.3 13.5 + - - +
49A LYS* 2.9 49.5 + - + +
38B GLN* 3.5 18.8 + - - +
41B GLU* 4.2 6.1 - - - +
42B GLU* 2.9 27.3 + - - +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 2.7 55.7 + - - +
39A TRP* 3.7 20.8 - - + -
44A THR* 3.2 8.6 + - - +
45A ASP* 1.3 78.2 - - - +
47A VAL* 1.3 57.9 + - - +
49A LYS* 3.5 9.1 + - - +
50A TRP* 3.1 26.7 + - - +
15B ARG* 4.9 5.0 + - - -
38B GLN* 5.5 5.4 + - - +
42B GLU* 4.6 0.4 + - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 3.8 37.7 - - + +
40A LEU* 4.4 11.0 - - + +
42A GLU 3.4 27.1 - - - +
43A SER* 5.1 1.3 - - - -
44A THR* 3.1 23.6 + - + +
46A GLU* 1.3 73.2 - - - +
48A ASP* 1.3 63.7 + - - +
50A TRP* 3.2 3.0 + - - +
51A THR* 2.8 42.7 + - + +
670A PHE* 4.4 14.1 - - + -
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Residues in contact with ASP 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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43A SER* 4.9 6.1 + - - -
44A THR 2.9 27.9 + - - +
45A ASP* 3.5 12.7 - - - +
47A VAL* 1.3 81.0 - - - +
49A LYS* 1.3 58.6 + - + +
51A THR* 3.2 7.8 + - - -
52A THR* 2.8 35.8 + - - +
693A LYS* 4.5 7.6 + - - +
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Residues in contact with LYS 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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45A ASP* 2.9 35.5 + - + +
46A GLU* 3.8 7.6 - - - +
48A ASP* 1.3 77.2 - - + +
50A TRP* 1.3 57.6 + - - +
52A THR* 3.4 5.3 + - - -
53A ALA* 2.8 30.0 + - - +
19B HIS* 5.4 12.1 - - - -
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Residues in contact with TRP 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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12A PRO* 4.6 4.9 - - + -
13A SER 3.7 14.8 - - - -
14A THR* 2.7 37.2 + - + +
39A TRP* 4.4 11.0 - + + -
40A LEU* 3.7 14.6 - - + -
46A GLU 3.1 17.5 + - - +
47A VAL* 3.2 5.6 + - - +
49A LYS* 1.3 73.7 - - - +
51A THR* 1.3 83.6 + - + +
53A ALA* 3.2 6.8 + - - +
54A GLN* 2.9 62.3 + - + +
670A PHE* 3.7 54.5 - + + -
673A ILE* 3.7 19.5 - - + -
674A ALA* 4.2 11.2 - - + -
689A ILE* 4.7 2.7 - - + -
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Residues in contact with THR 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 VAL* 2.8 25.8 + - + +
48A ASP* 3.2 8.1 + - - -
50A TRP* 1.3 92.9 - - + +
52A THR* 1.4 56.6 + - - +
54A GLN* 4.4 1.6 - - - -
55A ALA* 2.9 31.0 + - - +
670A PHE* 3.6 33.7 - - + -
691A ILE* 3.4 18.0 - - + +
693A LYS* 2.8 33.8 + - - -
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Residues in contact with THR 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 ASP* 2.8 23.2 + - - +
49A LYS* 3.7 6.3 - - - -
51A THR* 1.4 74.5 + - - +
53A ALA* 1.3 58.7 - - - +
55A ALA* 3.8 3.9 - - - +
56A ASP* 2.9 53.0 + - - +
693A LYS* 2.9 16.9 + - - +
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Residues in contact with ALA 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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12A PRO* 3.8 24.5 - - + +
49A LYS 2.8 18.0 + - - +
50A TRP* 3.6 5.8 - - - +
52A THR* 1.3 78.2 - - - +
54A GLN* 1.3 57.4 + - - +
56A ASP* 3.5 6.5 + - - +
57A LEU* 3.0 28.6 + - - +
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Residues in contact with GLN 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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12A PRO* 3.6 22.8 - - + +
14A THR* 4.3 0.6 + - - -
50A TRP* 2.9 60.5 + - + +
51A THR* 3.8 5.2 - - - +
53A ALA* 1.3 75.8 - - - +
55A ALA* 1.3 57.7 + - - +
57A LEU* 3.2 8.1 + - - +
58A ALA* 2.9 24.4 + - - +
673A ILE* 5.1 0.2 - - - -
677A GLN* 2.9 42.8 + - - +
688A LEU* 5.2 1.4 - - - +
689A ILE* 3.5 39.7 + - + +
691A ILE* 4.4 0.4 - - + -
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Residues in contact with ALA 55 (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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51A THR 2.9 21.4 + - - +
52A THR* 4.1 4.0 - - - +
54A GLN* 1.3 73.3 - - - +
56A ASP* 1.3 61.0 + - - +
58A ALA* 3.4 2.7 + - - +
59A GLN* 2.9 29.6 + - - +
689A ILE 3.8 8.3 + - - -
690A LYS* 4.7 7.9 - - + +
691A ILE* 4.0 26.0 - - + +
693A LYS* 6.1 2.5 - - - +
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Residues in contact with ASP 56 (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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52A THR* 2.9 40.5 + - - +
53A ALA* 3.7 7.0 - - - +
55A ALA* 1.3 78.9 - - - +
57A LEU* 1.3 56.9 + - - +
59A GLN* 3.5 5.3 + - - +
60A SER* 2.9 30.5 + - - -
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Residues in contact with LEU 57 (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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6A TRP* 4.1 27.4 - - + +
10A ASN* 3.8 22.4 - - - +
11A TYR* 3.7 30.3 - - + -
12A PRO* 3.8 13.9 - - + -
53A ALA 3.0 14.7 + - - +
54A GLN* 3.5 12.6 - - - +
56A ASP* 1.3 76.6 - - - +
58A ALA* 1.3 62.2 + - - +
60A SER* 3.3 10.5 + - - +
61A TYR* 3.0 20.8 + - - +
688A LEU* 3.9 16.8 - - + -
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Residues in contact with ALA 58 (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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54A GLN 2.9 16.0 + - - +
55A ALA* 3.8 4.3 - - - +
57A LEU* 1.3 75.4 - - - +
59A GLN* 1.4 65.5 + - - +
61A TYR* 3.1 4.2 + - - +
62A LEU* 3.0 30.3 + - + +
654A LEU* 4.4 8.7 - - + -
688A LEU* 4.0 30.0 - - + +
689A ILE 3.7 18.2 - - - +
690A LYS* 4.5 8.3 - - + -
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Residues in contact with GLN 59 (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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55A ALA 2.9 18.2 + - - +
56A ASP* 3.9 6.3 - - - +
58A ALA* 1.4 75.2 - - - +
60A SER* 1.3 58.2 + - - +
62A LEU* 4.0 10.1 - - - +
63A ASP* 2.9 61.3 + - - +
690A LYS* 4.8 8.0 - - + +
709A LYS* 3.2 21.2 + - - -
713A ASP* 4.4 1.7 - - - +
801A GOL 2.8 28.1 + - - -
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Residues in contact with SER 60 (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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6A TRP 5.1 4.7 + - - -
56A ASP 2.9 18.9 + - - -
57A LEU* 3.5 12.7 - - - +
58A ALA 3.3 0.2 - - - -
59A GLN* 1.3 76.8 - - - +
61A TYR* 1.3 62.6 + - - +
63A ASP* 3.3 23.2 + - - +
64A GLN* 3.5 17.4 + - - +
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Residues in contact with TYR 61 (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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6A TRP* 3.6 45.3 - + + +
57A LEU 3.0 12.9 + - - +
58A ALA 3.5 7.4 - - - +
60A SER* 1.3 77.9 + - - +
62A LEU* 1.3 67.0 + - + +
64A GLN* 3.0 43.1 + - + +
65A ASN* 4.0 3.0 + - + +
686A PRO* 3.7 26.4 - - + +
688A LEU* 3.9 24.0 - - + -
717A PHE* 3.9 19.3 - + - -
720A ARG* 4.4 28.2 + - + +
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Residues in contact with LEU 62 (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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58A ALA* 3.0 26.7 + - + +
59A GLN* 3.8 14.8 - - - +
61A TYR* 1.3 79.9 - - + +
63A ASP* 1.3 56.1 + - - +
65A ASN* 2.9 27.4 + - + +
68A ILE* 3.7 25.3 - - + +
654A LEU* 4.7 8.7 - - + -
688A LEU* 5.8 0.9 - - + -
690A LYS* 4.2 18.6 - - + -
713A ASP* 3.9 29.2 - - + +
717A PHE* 4.0 37.5 - - + -
801A GOL 3.2 14.6 - - - +
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Residues in contact with ASP 63 (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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59A GLN* 2.9 42.8 + - - +
60A SER* 3.4 14.5 - - - +
61A TYR 3.1 0.4 - - - -
62A LEU* 1.3 76.0 - - - +
64A GLN* 1.3 59.8 + - + +
65A ASN 3.1 4.2 + - - -
66A ALA* 4.9 1.4 + - - -
801A GOL 2.5 32.9 + - - +
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Residues in contact with GLN 64 (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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6A TRP 3.1 28.6 + - - +
60A SER* 3.6 18.6 + - - +
61A TYR* 3.0 32.5 + - - +
63A ASP* 1.3 76.3 - - + +
65A ASN* 1.3 56.5 + - - +
66A ALA* 3.7 3.4 + - - +
720A ARG* 3.4 19.3 + - - +
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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
------------------------------------------------------------
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