Contacts of the helix formed by residues 40 - 56 (chain P) in PDB entry 3FKS
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 40 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36P LYS 3.0 19.3 + - - +
37P ALA* 4.3 5.2 - - - -
38P LYS 2.5 26.2 + - - -
41P ALA* 1.3 63.3 + - - +
42P LYS* 2.9 8.1 - - - +
43P LYS* 3.2 17.6 - - - +
44P MET* 3.4 7.6 - - - -
17Q PRO 3.3 18.6 - - - +
18Q HIS* 3.5 16.7 - - - +
19Q GLU 4.5 6.1 - - - -
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Residues in contact with ALA 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ALA 3.8 9.1 + - - +
38P LYS* 3.0 6.9 - - + -
40P SER* 1.3 71.3 + - - +
42P LYS* 1.3 51.9 + - - +
43P LYS 3.3 0.2 - - - -
44P MET* 3.1 18.3 - - + -
45P ASP* 2.5 40.2 + - - +
219P LEU* 4.0 15.9 - - + +
220P THR* 3.5 26.2 - - + +
223P ALA* 4.7 4.3 - - + -
17Q PRO* 4.3 6.2 + - + +
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Residues in contact with LYS 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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38P LYS* 3.0 59.8 + - + +
40P SER* 2.9 1.0 - - - +
41P ALA* 1.3 76.8 - - - +
43P LYS* 1.3 62.1 + - + +
45P ASP* 3.2 14.5 + - - +
46P GLU* 3.1 24.6 + - - +
168P ASP* 5.2 3.9 + - - -
224P GLN* 3.3 23.5 - - - +
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Residues in contact with LYS 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P SER* 3.2 9.3 - - - +
42P LYS* 1.3 75.6 - - + +
44P MET* 1.3 61.7 + - - +
45P ASP 3.0 5.9 + - - -
46P GLU* 3.4 22.4 + - - +
47P ALA* 3.3 21.0 + - - +
15Q ALA* 6.4 0.4 - - - -
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Residues in contact with MET 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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40P SER* 3.4 4.7 - - - -
41P ALA* 2.9 23.8 + - - +
43P LYS* 1.3 77.6 - - - +
45P ASP* 1.3 58.8 + - - +
47P ALA* 4.1 8.7 - - + +
48P GLU* 3.6 19.1 + - - +
140P PHE* 5.9 0.7 - - + -
212P TYR* 4.4 12.8 - - + +
216P ASN* 3.0 44.7 - - - +
219P LEU* 6.0 4.3 - - - -
220P THR* 5.4 2.9 - - - +
15Q ALA* 4.4 15.7 - - + +
16Q LEU 2.8 30.3 - - - +
17Q PRO* 3.5 23.1 - - + +
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Residues in contact with ASP 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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41P ALA 2.5 17.7 + - - +
42P LYS* 3.3 10.1 - - - +
43P LYS 3.0 0.2 - - - -
44P MET* 1.3 75.4 - - - +
46P GLU* 1.3 55.7 + - - +
47P ALA 3.2 1.3 - - - -
48P GLU* 3.2 5.9 + - - +
49P GLN* 2.7 60.2 + - - +
216P ASN* 5.7 0.2 - - - -
217P GLN* 3.1 27.0 + - - +
220P THR* 3.9 16.0 - - + +
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Residues in contact with GLU 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 LYS* 3.1 15.3 - - - +
43P LYS* 3.6 29.3 + - - +
45P ASP* 1.3 78.0 - - + +
47P ALA* 1.3 53.8 + - - +
49P GLN* 4.3 4.5 - - - +
50P LEU* 2.5 46.1 + - + +
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Residues in contact with ALA 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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43P LYS 3.3 12.9 + - - +
44P MET* 4.3 10.3 - - + +
46P GLU* 1.3 80.6 - - - +
48P GLU* 1.3 59.9 + - - +
49P GLN 3.5 0.3 + - - -
50P LEU* 3.9 10.4 + - - +
51P PHE* 4.3 9.2 + - - +
76Q THR* 5.1 7.8 - - - -
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Residues in contact with GLU 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 MET 3.6 16.6 + - - +
45P ASP* 3.2 9.2 + - - +
47P ALA* 1.3 78.5 - - - +
49P GLN* 1.3 58.1 + - - +
51P PHE* 4.9 4.6 - - - +
52P TYR* 2.9 27.5 + - - -
212P TYR* 5.3 7.4 - - + +
213P THR* 4.3 15.4 - - + +
216P ASN* 3.9 16.6 - - + +
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Residues in contact with GLN 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 ASP* 2.7 40.9 + - - +
46P GLU* 3.3 4.0 - - - +
48P GLU* 1.3 80.2 - - - +
50P LEU* 1.3 59.0 + - - +
51P PHE 3.4 1.6 - - - -
52P TYR* 3.3 16.1 - - + +
53P LYS* 2.9 25.7 + - + +
183P PHE* 6.3 0.6 - - - -
217P GLN* 5.0 7.3 + - - -
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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 GLU* 2.5 26.9 + - + +
47P ALA* 3.9 7.6 + - - +
48P GLU 3.7 0.2 - - - -
49P GLN* 1.3 71.1 - - - +
51P PHE* 1.3 65.5 + - - +
52P TYR 3.0 0.9 - - - -
53P LYS* 3.0 30.1 + - + +
54P ASN* 3.2 26.8 + - - +
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Residues in contact with PHE 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 ALA 4.3 8.0 + - - +
48P GLU 4.9 3.4 - - - +
50P LEU* 1.3 77.3 - - - +
52P TYR* 1.3 85.8 + + - +
54P ASN* 3.3 22.1 + - + +
55P ALA* 3.3 25.2 + - + +
188P ILE* 4.3 20.6 - - + -
194P PHE* 6.1 4.5 - + - -
209P LEU* 3.9 25.1 - - + -
49Q VAL* 3.5 34.8 - - + -
76Q THR* 4.3 19.1 - - - -
77Q VAL 4.8 12.1 - - - -
78Q GLN* 5.9 0.4 - - - -
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Residues in contact with TYR 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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48P GLU 2.9 26.0 - - - -
49P GLN* 3.3 25.0 + - + +
50P LEU 3.0 0.8 - - - -
51P PHE* 1.3 94.7 - + - +
53P LYS* 1.3 52.8 + - - +
55P ALA* 5.1 1.3 - - + -
56P GLU* 2.6 41.8 + - - +
183P PHE* 3.8 42.6 + + + +
188P ILE* 3.6 23.6 - - + +
191P SER* 6.0 0.9 - - - -
209P LEU* 3.0 30.2 - - + +
213P THR* 3.3 28.3 + - + -
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Residues in contact with LYS 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 GLN* 2.9 13.6 + - + +
50P LEU* 3.0 25.5 + - + +
52P TYR* 1.3 74.5 - - - +
54P ASN* 1.3 64.6 + - - +
56P GLU* 2.9 28.6 - - + +
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Residues in contact with ASN 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* 3.2 22.6 + - - +
51P PHE* 3.3 13.2 + - - +
53P LYS* 1.3 79.4 - - - +
55P ALA* 1.3 58.0 + - - +
56P GLU* 2.8 22.3 - - - +
193P SER* 2.9 21.2 - - - +
77Q VAL 5.0 2.5 + - - +
78Q GLN* 3.1 35.5 - - - +
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Residues in contact with ALA 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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51P PHE* 3.3 27.9 + - + +
52P TYR* 4.6 1.1 - - + +
54P ASN* 1.3 77.4 - - - +
56P GLU* 1.3 70.0 + - - +
188P ILE* 4.9 2.7 - - + +
191P SER* 3.2 18.3 - - - +
192P PRO* 3.1 25.3 - - - +
193P SER 3.1 22.6 + - - +
194P PHE* 5.0 5.2 - - + -
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Residues in contact with GLU 56 (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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52P TYR* 2.6 33.3 + - - -
53P LYS* 2.9 22.0 - - + +
54P ASN* 2.8 20.9 - - - +
55P ALA* 1.3 77.5 - - - +
183P PHE* 5.6 11.0 - - - -
187P THR* 5.0 2.6 - - - +
191P SER* 3.3 17.4 + - - -
192P PRO* 3.6 34.2 - - + +
193P SER* 4.4 3.8 + - - -
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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