Contacts of the helix formed by residues 46 - 63 (chain D) in PDB entry 1F5Q
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 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D GLN* 3.1 19.2 + - - -
43D HIS 2.8 18.2 + - - -
44D PHE 3.3 2.0 - - - +
45D THR* 1.3 80.3 - - - +
47D GLN* 1.3 65.2 + - - +
48D TYR* 3.3 33.3 - - - -
49D ARG* 3.4 16.6 + - - +
50D LYS* 3.7 12.3 + - - +
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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
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45D THR 3.7 1.6 + - - -
46D SER* 1.3 73.7 - - - +
48D TYR* 1.3 59.0 + - - +
50D LYS* 2.9 34.2 + - - +
51D VAL* 3.4 21.0 + - - +
247D TYR* 2.5 32.4 + - - +
251D ASN* 2.9 27.1 + - - +
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Residues in contact with TYR 48 (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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42D GLN 5.2 0.2 - - - -
43D HIS* 2.5 42.1 + + - +
46D SER* 3.2 29.0 - - - -
47D GLN* 1.3 83.8 - - - +
49D ARG* 1.3 62.6 - - - +
51D VAL* 3.5 7.6 + - - +
52D LEU* 3.3 28.9 + - + +
81D PHE* 3.5 27.9 - + - -
91D TYR* 3.7 42.8 + + + -
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Residues in contact with ARG 49 (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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43D HIS* 3.5 34.8 - - + +
44D PHE* 3.3 25.4 - - - +
46D SER* 3.4 8.1 + - - +
47D GLN 3.2 1.0 - - - -
48D TYR* 1.3 87.8 - - + +
50D LYS* 1.3 56.2 + - - +
52D LEU* 4.0 4.9 - - - +
53D THR* 2.7 45.9 + - + +
74D VAL* 3.6 12.9 - - - +
77D LEU* 5.3 4.5 - - + -
78D ASP* 2.8 40.5 + - - +
182D LEU 2.8 29.3 + - - -
183D CYS 3.9 15.0 + - - -
185D GLY 4.1 7.3 - - - +
188D ALA* 3.5 16.3 + - - +
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Residues in contact with LYS 50 (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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44D PHE 5.3 2.3 + - - +
45D THR* 3.7 15.0 + - - +
46D SER 3.7 13.4 + - - +
47D GLN* 2.9 27.7 + - - +
49D ARG* 1.3 78.6 - - + +
51D VAL* 1.3 53.8 + - - +
53D THR* 3.4 3.9 + - - -
54D THR* 2.6 42.6 + - + +
183D CYS 4.4 14.6 - - - +
185D GLY 6.1 1.8 - - - +
186D ARG* 5.7 3.6 - - - +
247D TYR* 3.4 45.3 - - + -
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN* 3.4 28.5 + - - +
48D TYR* 3.5 9.2 + - - +
49D ARG 3.3 0.2 - - - -
50D LYS* 1.3 77.6 - - - +
52D LEU* 1.3 66.1 + - + +
54D THR* 2.8 18.5 + - - -
55D TRP* 2.8 21.2 + - + +
92D GLN* 5.3 5.4 - - - +
247D TYR* 4.0 11.0 - - + -
248D PHE* 3.2 31.7 - - + +
251D ASN* 4.4 12.6 - - + +
252D ALA* 6.2 0.4 - - - -
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Residues in contact with LEU 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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48D TYR* 3.3 22.9 + - + +
49D ARG* 4.2 4.3 - - - +
51D VAL* 1.3 80.8 - - + +
53D THR* 1.3 59.9 + - - +
55D TRP* 3.3 4.1 + - + +
56D MET* 3.0 33.1 + - - +
77D LEU* 4.2 14.1 - - + -
81D PHE* 3.6 35.9 - - + -
91D TYR* 3.7 24.0 - - + +
92D GLN* 3.9 24.7 - - - +
95D ALA* 3.8 21.3 - - + -
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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
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49D ARG* 2.7 51.5 + - + +
50D LYS* 3.4 7.1 + - - -
52D LEU* 1.3 73.2 - - - +
54D THR* 1.3 67.0 + - - +
56D MET* 3.5 5.9 + - - -
57D PHE* 3.0 24.1 + - - +
70D PHE* 3.4 7.0 - - - -
74D VAL* 4.0 23.6 - - + -
77D LEU* 4.5 10.3 - - + -
182D LEU 4.2 2.5 - - - +
183D CYS* 3.8 27.2 + - - +
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Residues in contact with THR 54 (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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50D LYS* 2.6 29.3 + - + +
51D VAL* 2.8 15.8 + - - -
53D THR* 1.3 79.7 + - - +
55D TRP* 1.3 60.2 + - - +
57D PHE* 3.5 9.1 - - - +
58D CYS* 3.3 27.9 + - - -
183D CYS* 4.5 16.6 - - + +
243D PHE* 4.5 7.9 - - + -
244D ASP 3.8 21.1 - - - +
245D GLU* 4.2 2.8 - - - +
247D TYR* 3.7 12.3 - - + +
248D PHE* 3.5 18.0 + - - -
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Residues in contact with TRP 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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51D VAL* 2.8 18.7 + - + +
52D LEU* 3.3 6.3 - - - +
53D THR 3.1 0.2 - - - -
54D THR* 1.3 73.7 + - - +
56D MET* 1.3 78.1 + - + +
57D PHE 3.0 0.9 - - - -
58D CYS* 2.8 24.6 + - - +
59D VAL* 2.9 32.8 + - + +
92D GLN* 3.4 37.1 + - - +
95D ALA* 4.0 6.1 - - + -
96D ALA* 3.9 24.0 - - + -
99D LEU* 3.9 16.4 - - + -
116D LEU* 4.3 10.1 - - + -
119D LEU* 4.3 25.5 + - + +
120D CYS* 3.9 19.7 - - - -
248D PHE* 3.7 36.6 - + + -
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Residues in contact with MET 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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52D LEU 3.0 18.6 + - - +
53D THR* 3.8 7.6 - - - +
55D TRP* 1.3 89.6 - - + +
57D PHE* 1.3 57.7 + - - +
59D VAL* 3.2 1.2 + - - +
60D CYS* 2.8 34.1 + - - +
70D PHE* 4.1 8.3 - - + -
73D ALA* 3.3 37.7 - - + +
74D VAL* 4.7 7.4 - - - -
77D LEU* 4.0 22.2 - - + -
95D ALA* 3.2 27.6 - - + +
98D ALA* 3.7 13.0 - - + -
99D LEU* 3.5 25.1 - - + -
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Residues in contact with PHE 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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53D THR 3.0 17.7 + - - +
54D THR* 3.5 12.6 - - - +
56D MET* 1.3 78.0 - - - +
58D CYS* 1.3 61.6 + - - +
60D CYS* 3.7 3.3 - - - +
61D LYS* 2.9 42.0 + - + +
70D PHE* 3.6 34.7 - + + -
179D PHE* 3.9 26.9 - + + -
180D CYS* 6.5 0.4 - - - -
183D CYS* 4.9 2.0 - - - -
243D PHE* 3.7 29.8 - + - -
245D GLU* 3.6 36.1 - - + -
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Residues in contact with CYS 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 THR 3.3 4.0 + - - -
55D TRP 2.8 14.1 + - - +
57D PHE* 1.3 81.7 - - - +
59D VAL* 1.3 68.4 + - + +
61D LYS* 3.0 10.5 + - - +
62D ASP* 2.9 36.6 + - - +
245D GLU* 3.3 22.9 - - - -
246D ASN* 5.2 2.7 - - - -
248D PHE* 3.2 36.8 - - + -
249D LYS* 5.5 2.0 - - - -
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Residues in contact with VAL 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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55D TRP* 2.9 55.0 + - + +
56D MET 3.6 5.8 - - - +
58D CYS* 1.3 75.6 - - + +
60D CYS* 1.3 64.4 + - - +
62D ASP* 3.4 4.7 + - - +
63D LEU* 3.0 45.9 + - + +
65D GLN* 6.1 0.4 - - + -
99D LEU* 3.8 17.9 - - + -
111D ILE* 5.3 2.2 - - + -
116D LEU* 4.1 8.7 - - + -
119D LEU* 4.1 20.6 - - + -
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Residues in contact with CYS 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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56D MET 2.8 20.2 + - - +
57D PHE 3.7 4.5 - - - +
59D VAL* 1.3 79.1 - - - +
61D LYS* 1.3 60.0 + - - +
64D ARG* 3.4 1.2 + - - -
65D GLN* 2.9 47.7 + - + +
66D ASP 5.5 1.3 - - - +
69D VAL* 4.1 11.2 - - - -
70D PHE* 3.9 32.1 - - + -
99D LEU* 3.7 25.8 - - - -
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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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57D PHE* 2.9 39.7 + - + +
58D CYS* 3.0 12.2 + - - +
60D CYS* 1.3 77.0 - - - +
62D ASP* 1.3 83.2 + - - +
64D ARG* 3.2 20.5 + - - +
245D GLU* 4.4 21.0 + - - +
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Residues in contact with ASP 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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58D CYS* 2.9 26.2 + - - +
59D VAL* 4.0 4.2 - - - +
61D LYS* 1.3 93.1 + - - +
63D LEU* 1.3 67.3 + - + +
64D ARG* 3.0 17.7 + - - +
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Residues in contact with LEU 63 (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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59D VAL* 3.0 32.0 + - + +
62D ASP* 1.3 82.3 - - + +
64D ARG* 1.3 71.0 + - - +
65D GLN* 2.8 27.1 + - + +
109D MET* 4.2 8.1 - - - +
111D ILE* 3.8 34.8 - - + -
115D GLN* 3.6 27.4 - - - +
119D LEU* 4.8 10.1 - - + -
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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