Contacts of the helix formed by residues 41 - 55 (chain P) in PDB entry 5LN3
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 GLN 41 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P LYS* 4.3 9.4 + - - +
37P GLU* 3.7 36.7 + - - +
40P LEU* 1.3 83.3 - - - +
42P GLU* 1.4 92.1 + - + +
43P VAL 3.4 2.2 - - - -
44P ILE* 3.6 3.6 - - - +
45P GLU* 3.2 33.9 + - - +
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Residues in contact with GLU 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P GLU* 3.4 30.5 + - - +
41P GLN* 1.4 98.7 - - + +
43P VAL* 1.3 63.5 + - + +
45P GLU* 4.3 1.0 - - - +
46P THR* 3.0 35.6 + - - +
73P MET* 4.2 19.6 - - + +
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Residues in contact with VAL 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P GLU* 3.8 14.2 + - + +
38P GLY 3.6 12.8 - - - +
41P GLN 3.4 0.4 - - - -
42P GLU* 1.3 79.9 - - + +
44P ILE* 1.3 59.0 + - - +
46P THR* 3.3 9.1 - - + +
47P LEU* 2.9 41.4 + - + +
70P VAL* 4.8 6.1 - - + +
73P MET* 4.2 22.7 - - + +
74P CYS* 3.7 28.9 - - + +
77P ALA* 3.9 23.8 - - + -
78P LYS* 4.0 4.9 - - - +
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Residues in contact with ILE 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P GLY 4.2 2.6 + - - +
39P ARG* 3.7 31.9 - - + +
40P LEU* 4.0 2.5 - - - -
41P GLN 3.6 25.5 - - - +
43P VAL* 1.3 78.2 - - - +
45P GLU* 1.4 76.8 + - + +
47P LEU* 3.1 21.5 + - + +
48P LEU* 3.1 38.4 + - + +
86P ASN* 5.5 7.0 - - - +
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Residues in contact with GLU 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P LEU 5.8 0.7 - - - -
41P GLN* 3.2 20.3 + - - +
42P GLU* 4.4 1.8 - - - +
44P ILE* 1.4 86.7 - - + +
46P THR* 1.4 63.2 + - - +
48P LEU* 3.3 31.4 + - - +
49P SER* 3.3 20.6 + - - -
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Residues in contact with THR 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P GLU 3.0 25.9 + - - +
43P VAL* 3.3 14.4 - - + +
45P GLU* 1.4 77.5 - - - +
47P LEU* 1.4 59.3 + - - +
49P SER* 3.6 4.9 + - - -
50P LEU* 3.2 25.6 + - - +
66P ILE* 4.8 10.7 - - - +
70P VAL* 3.8 25.0 - - + +
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Residues in contact with LEU 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P GLY 6.0 0.4 - - - +
43P VAL* 2.9 35.3 + - + +
44P ILE* 3.1 24.7 + - + +
46P THR* 1.4 75.6 - - - +
48P LEU* 1.3 64.3 + - + +
50P LEU* 3.5 4.7 + - + +
51P GLU* 3.1 40.0 + - + +
70P VAL* 4.1 28.0 - - + -
74P CYS* 5.3 7.2 - - + -
78P LYS* 6.1 0.4 - - - +
86P ASN* 5.3 10.5 - - + +
90P LEU* 4.0 32.1 - - + -
93P ARG* 5.0 5.4 - - - +
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Residues in contact with LEU 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P ILE* 3.1 27.3 + - + +
45P GLU* 3.3 29.8 + - - +
47P LEU* 1.3 77.0 - - + +
49P SER* 1.4 61.6 + - - +
51P GLU* 3.8 13.7 - - - +
52P LYS* 3.1 22.9 + - - +
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Residues in contact with SER 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P GLU 3.3 16.1 + - - -
46P THR* 4.1 6.2 - - - -
48P LEU* 1.4 73.7 - - - +
50P LEU* 1.4 60.7 + - - +
52P LYS* 3.5 8.9 + - - +
53P GLN* 3.1 27.0 + - - +
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Residues in contact with LEU 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P THR 3.2 15.6 + - - +
47P LEU* 3.8 6.5 - - + +
49P SER* 1.4 78.2 - - - +
51P GLU* 1.4 57.1 + - + +
53P GLN* 2.9 12.4 + - - +
54P THR* 2.8 62.4 + - - +
62P SER* 4.0 10.3 - - - +
66P ILE* 3.7 50.5 - - + +
67P LEU* 4.2 14.1 - - + +
70P VAL* 3.6 34.3 - - + -
96P GLN* 5.8 0.9 - - - +
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Residues in contact with GLU 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P LEU* 3.1 37.6 + - + +
48P LEU* 3.8 14.8 + - - +
50P LEU* 1.4 79.6 - - + +
52P LYS* 1.4 59.0 + - - +
54P THR* 3.8 5.8 - - - -
55P ARG* 3.0 29.6 + - - -
90P LEU* 5.4 2.5 - - + -
93P ARG* 3.1 60.8 + - + +
95P SER* 4.7 9.0 - - - +
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Residues in contact with LYS 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ALA* 2.9 30.6 + - - +
244A GLU* 3.6 22.9 - - + +
246A ASP* 3.9 16.2 + - - +
48P LEU 3.1 11.9 + - - +
49P SER* 3.5 11.9 - - - +
50P LEU 3.2 0.2 - - - -
51P GLU* 1.4 78.2 - - - +
53P GLN* 1.4 61.1 + - - +
55P ARG* 3.3 19.6 - - - +
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Residues in contact with GLN 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P SER* 3.1 15.2 + - - +
50P LEU* 2.9 20.6 + - - +
52P LYS* 1.4 73.7 - - - +
54P THR* 1.3 60.8 + - - +
55P ARG* 3.9 5.2 - - - +
61P VAL* 3.3 21.8 + - + +
62P SER* 3.1 32.9 + - - +
66P ILE* 5.5 7.5 - - - +
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Residues in contact with THR 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P LEU* 2.8 32.1 + - - +
51P GLU* 3.8 6.5 - - - -
53P GLN* 1.3 68.6 - - - +
55P ARG* 1.4 81.0 + - - +
58P SER* 4.1 4.0 - - - -
59P ASP 3.9 7.8 - - - +
61P VAL* 3.2 17.8 - - + +
62P SER* 3.2 17.6 + - - +
67P LEU* 6.1 1.1 - - + -
95P SER* 3.8 17.3 - - - -
96P GLN* 3.6 33.5 + - + +
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Residues in contact with ARG 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ASP* 3.0 50.7 + - - +
51P GLU 3.0 14.8 + - - -
52P LYS 3.3 18.6 - - - +
53P GLN 3.9 5.8 - - - +
54P THR* 1.4 99.6 - - - +
56P THR* 1.4 58.4 + - - +
57P ALA* 3.3 21.7 - - + +
58P SER* 3.5 30.0 + - - +
61P VAL* 5.1 4.3 - - - -
95P SER* 4.0 6.1 + - - -
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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