Contacts of the helix formed by residues 45 - 59 (chain A) in PDB entry 1N54
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 SER 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A CYS* 1.3 79.1 - - - +
46A LEU* 1.3 63.1 + - - +
47A GLU* 3.2 21.1 + - - +
48A SER* 2.4 44.2 + - - -
49A ASN* 3.4 6.3 + - - +
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Residues in contact with LEU 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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38A VAL* 3.8 18.8 - - + +
42A SER* 5.4 2.2 - - - -
44A CYS 3.7 2.0 + - - -
45A SER* 1.3 73.4 - - - +
47A GLU* 1.3 70.4 + - - +
49A ASN* 3.4 6.9 + - + +
50A LEU* 3.0 33.1 + - + +
85A ILE* 3.6 53.2 - - + -
250A LEU* 6.0 7.9 - - + -
252A PRO* 4.1 20.9 - - + -
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Residues in contact with GLU 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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45A SER* 3.1 19.1 + - - +
46A LEU* 1.3 87.9 + - - +
48A SER* 1.3 53.2 + - - +
50A LEU* 3.1 5.8 + - + +
51A GLU* 2.7 36.8 + - - +
251A ARG 5.4 0.5 - - - +
252A PRO* 4.2 17.3 - - - +
255A ALA* 4.2 25.1 - - + +
256A PHE* 3.7 25.1 - - + -
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Residues in contact with SER 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 CYS* 3.0 29.8 - - - -
45A SER* 2.4 33.5 + - - -
47A GLU* 1.3 77.8 - - - +
49A ASN* 1.3 54.4 + - - +
51A GLU* 3.7 5.6 - - - +
52A GLY* 2.6 35.2 + - - -
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Residues in contact with ASN 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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37A LYS* 4.0 18.8 + - - +
38A VAL* 3.7 27.3 + - + +
42A SER* 4.2 21.3 + - - -
44A CYS* 4.0 14.2 - - - +
45A SER 3.7 10.4 - - - +
46A LEU* 3.4 11.2 + - - +
47A GLU 3.2 0.6 - - - -
48A SER* 1.3 86.7 + - - +
50A LEU* 1.3 58.6 + - - +
52A GLY* 5.1 0.4 - - - -
53A LEU* 2.9 30.5 + - - +
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Residues in contact with LEU 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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38A VAL* 4.9 9.2 - - + -
46A LEU* 3.0 33.4 + - + +
47A GLU* 3.5 7.0 - - - +
49A ASN* 1.3 75.0 - - - +
51A GLU* 1.3 59.8 + - - +
53A LEU* 3.1 5.8 + - - +
54A ALA* 2.8 29.2 + - - +
85A ILE* 3.3 28.7 - - + +
88A THR* 3.8 23.8 - - + -
89A LEU* 3.7 32.1 - - + +
92A LEU* 5.2 4.6 - - + +
252A PRO* 3.8 19.1 - - + -
256A PHE* 4.2 13.5 - - + -
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Residues in contact with GLU 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 GLU 2.7 20.3 + - - +
48A SER* 3.7 7.6 - - - +
50A LEU* 1.3 72.1 - - - +
52A GLY* 1.3 64.5 + - - +
54A ALA* 2.9 23.7 - - - +
55A GLY 3.6 2.8 + - - -
92A LEU* 4.8 4.0 - - - +
96A ARG* 2.6 34.7 + - - -
256A PHE* 3.8 22.2 - - + -
259A ILE* 3.8 23.9 - - - +
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Residues in contact with GLY 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 SER 2.6 21.7 + - - -
49A ASN* 4.2 0.7 - - - -
51A GLU* 1.3 76.3 - - - +
53A LEU* 1.3 62.4 + - - +
54A ALA 3.0 1.0 + - - -
55A GLY* 3.5 1.6 + - - -
56A VAL* 3.0 25.4 + - - +
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Residues in contact with LEU 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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34A LEU* 3.7 31.2 - - + +
35A ILE* 4.2 5.6 - - + -
38A VAL* 3.3 27.8 - - + -
49A ASN 2.9 20.1 + - - +
50A LEU* 3.1 4.5 + - - +
52A GLY* 1.3 74.6 - - - +
54A ALA* 1.3 61.2 + - - +
56A VAL* 3.4 10.9 + - + -
57A LEU* 3.0 55.3 + - + +
89A LEU* 3.4 37.2 - - + -
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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 LEU 2.8 12.7 + - - +
51A GLU* 2.9 20.2 - - - +
52A GLY 3.0 1.2 - - - -
53A LEU* 1.3 78.7 - - - +
55A GLY* 1.3 56.2 + - - +
56A VAL 3.1 0.5 + - - -
57A LEU* 3.2 2.1 + - - +
58A GLU* 2.8 29.4 + - - +
89A LEU* 4.5 1.8 - - + +
92A LEU* 4.3 19.1 - - + -
93A LEU* 4.0 15.8 - - + +
96A ARG* 3.8 20.9 - - - +
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Residues in contact with GLY 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 GLU 3.6 2.8 + - - -
52A GLY 3.5 5.1 + - - -
54A ALA* 1.3 79.4 - - - +
56A VAL* 1.3 57.1 + - - +
58A GLU* 4.2 3.4 - - - -
59A ALA* 2.8 35.0 + - - +
96A ARG* 3.1 22.5 - - - +
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Residues in contact with VAL 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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31A LEU* 5.3 1.8 - - + -
34A LEU* 4.4 24.2 - - + -
52A GLY 3.0 20.6 - - - +
53A LEU* 3.4 15.5 - - + +
54A ALA 3.0 0.4 - - - -
55A GLY* 1.3 80.8 - - - +
57A LEU* 1.3 66.9 + - + +
59A ALA* 3.6 4.0 - - - +
60A ASP* 3.2 35.6 + - - +
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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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31A LEU* 3.6 29.6 - - + -
34A LEU* 5.8 0.4 - - + -
35A ILE* 4.1 9.9 - - + -
53A LEU* 3.0 46.6 + - + +
54A ALA 3.8 2.0 - - - +
56A VAL* 1.3 79.8 - - + +
58A GLU* 1.3 61.7 + - - +
60A ASP* 2.9 18.5 + - - +
61A LEU* 3.1 13.5 + - + +
68A ILE* 3.5 35.2 - - + +
72A LEU* 4.9 0.7 - - + -
89A LEU* 4.0 22.9 - - + -
93A LEU* 4.1 18.4 - - + -
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Residues in contact with GLU 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 ALA 2.8 15.8 + - - +
55A GLY* 4.0 2.5 - - - +
57A LEU* 1.3 72.0 - - - +
59A ALA* 1.3 59.6 + - - +
60A ASP 2.9 10.2 + - - -
61A LEU* 3.0 32.4 + - + +
62A PRO* 3.4 10.6 - - - +
93A LEU* 5.1 6.0 - - + +
96A ARG* 2.8 65.4 + - + +
97A ASN* 5.2 2.0 - - + +
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Residues in contact with ALA 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 GLY 2.8 25.2 + - - +
56A VAL* 3.6 7.2 - - - +
58A GLU* 1.3 74.0 - - - +
60A ASP* 1.3 65.6 + - - +
61A LEU 3.5 0.4 - - - -
62A PRO* 4.1 8.0 - - - +
63A ASN* 4.2 10.4 - - - +
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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