Contacts of the helix formed by residues 48 - 67 (chain A) in PDB entry 1FQY
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 ASP 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.9 8.7 - - - -
43A GLN* 3.7 22.3 + - - +
44A THR* 5.4 0.4 + - - -
46A VAL 3.7 1.8 + - - -
47A GLN* 1.3 66.5 - - - +
49A ASN* 1.3 57.6 + - - +
50A VAL* 3.0 6.4 + - + +
51A LYS* 2.6 62.8 + - - +
52A VAL* 4.2 0.2 - - - -
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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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46A VAL* 5.5 5.2 + - - +
47A GLN* 2.8 17.7 + - - +
48A ASP* 1.3 68.9 - - - +
50A VAL* 1.3 64.2 + - + +
51A LYS 3.5 0.2 - - - -
52A VAL* 3.1 15.8 - - - +
53A SER* 3.0 16.9 + - - -
181A LEU* 5.4 3.8 - - - +
184A ILE* 3.8 34.0 - - + +
185A ASP* 5.8 6.0 - - - +
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Residues in contact with VAL 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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48A ASP* 3.0 7.9 + - + +
49A ASN* 1.3 69.1 - - + +
51A LYS* 1.3 71.5 + - + +
52A VAL 2.8 2.0 - - - -
53A SER* 2.6 12.6 + - - -
54A LEU* 2.5 47.0 + - + +
181A LEU* 5.8 10.8 - - + +
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Residues in contact with LYS 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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31A SER* 4.7 1.5 + - - -
35A PHE* 3.1 55.6 - - + +
47A GLN* 2.8 29.3 + - - +
48A ASP* 2.6 50.3 + - - +
50A VAL* 1.3 79.5 - - + +
52A VAL* 1.3 83.9 - - - +
54A LEU* 2.8 23.0 + - + +
55A ALA* 2.8 24.3 + - - +
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Residues in contact with VAL 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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31A SER* 4.9 2.7 - - - -
32A ALA* 3.9 20.2 - - + +
47A GLN* 2.8 33.2 - - - +
49A ASN* 3.1 23.3 - - - +
51A LYS* 1.3 99.5 - - + +
53A SER* 1.3 58.2 + - - +
55A ALA* 3.3 9.3 + - - +
56A PHE* 2.6 51.1 + - + -
184A ILE* 5.2 11.0 - - + -
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Residues in contact with SER 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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49A ASN 3.0 8.0 + - - -
50A VAL* 2.6 24.6 + - - -
52A VAL* 1.3 73.4 - - - +
54A LEU* 1.3 49.4 + - - -
56A PHE* 3.2 3.4 + - - +
57A GLY* 2.5 37.1 + - - -
177A ALA* 3.2 9.0 + - - -
180A HIS* 3.2 13.1 + - - +
181A LEU* 2.9 51.1 + - - +
184A ILE* 6.1 2.6 - - - +
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Residues in contact with LEU 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 VAL* 2.5 28.7 + - + +
51A LYS* 2.8 26.4 + - + +
53A SER* 1.3 74.1 - - - +
55A ALA* 1.3 54.6 + - - +
57A GLY* 4.2 1.3 - - - +
58A LEU* 2.5 64.9 + - + +
177A ALA* 5.8 4.7 - - + -
181A LEU* 6.5 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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27A ILE* 4.9 8.3 - - + +
28A SER* 4.6 7.0 - - - -
31A SER* 2.8 35.7 - - - +
51A LYS 2.8 11.6 + - - +
52A VAL 3.3 7.8 + - - +
54A LEU* 1.3 72.6 - - - +
56A PHE* 1.3 67.4 + - + +
58A LEU* 5.4 0.7 - - - -
59A SER* 2.6 30.9 + - - +
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Residues in contact with PHE 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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24A PHE* 4.4 17.7 - + + -
28A SER* 3.3 44.2 - - - -
29A ILE* 4.9 1.6 - - - -
32A ALA* 4.6 6.3 - - + -
52A VAL* 2.6 52.9 - - + -
53A SER* 3.8 3.6 - - - +
55A ALA* 1.3 81.0 - - + +
57A GLY* 1.3 64.6 + - - +
59A SER* 3.5 3.5 - - - -
60A ILE* 3.3 24.1 - - - +
128A ASP* 4.8 13.0 - - + -
180A HIS* 3.4 28.5 - + + +
184A ILE* 4.9 10.3 - - + -
189A CYS* 3.9 26.5 - - - -
195A ARG* 6.3 0.4 - - + -
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Residues in contact with GLY 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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53A SER 2.5 23.5 + - - -
54A LEU* 3.3 0.9 - - - -
55A ALA 3.1 1.0 - - - -
56A PHE* 1.3 73.3 - - - +
58A LEU* 1.3 66.0 + - - +
60A ILE* 3.9 4.3 + - - +
173A GLY* 3.0 26.6 - - - +
177A ALA* 3.7 28.3 - - - -
180A HIS* 4.3 1.8 - - - -
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Residues in contact with LEU 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 LEU* 2.5 52.9 + - + +
55A ALA* 5.4 0.9 - - - -
57A GLY* 1.3 69.4 - - - +
59A SER* 1.3 66.9 + - - +
61A ALA* 2.9 19.5 + - - +
62A THR* 3.4 12.6 + - - +
174A LEU* 3.6 28.3 - - + -
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Residues in contact with SER 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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24A PHE* 4.1 15.7 + - - -
27A ILE* 3.5 29.2 - - - +
28A SER 5.0 0.2 + - - -
55A ALA* 2.6 25.1 + - - -
56A PHE* 3.5 6.0 - - - -
57A GLY 3.3 0.2 - - - -
58A LEU* 1.3 76.2 - - - +
60A ILE* 1.3 64.6 - - - +
62A THR* 3.0 19.2 + - - -
63A LEU* 3.1 24.7 + - - +
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Residues in contact with ILE 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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24A PHE* 3.7 28.7 - - + -
56A PHE 3.3 18.6 + - - +
57A GLY 4.3 3.6 - - - +
58A LEU 3.1 0.8 + - - -
59A SER* 1.3 74.1 - - - +
61A ALA* 1.3 52.4 + - - +
63A LEU* 3.5 4.0 + - - +
64A ALA* 2.8 42.6 + - + +
74A HIS* 5.9 2.2 - - - -
75A LEU* 3.4 29.1 - - + +
172A ILE* 5.7 4.9 - - + -
173A GLY* 4.7 5.2 - - - -
176A VAL* 3.5 39.9 - - + -
180A HIS* 4.7 3.1 - - + +
191A ILE* 6.1 0.7 - - + -
192A ASN* 6.1 2.0 - - - +
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Residues in contact with ALA 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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58A LEU* 2.9 13.1 + - - +
60A ILE* 1.3 75.5 - - - +
62A THR* 1.3 66.0 + - - +
64A ALA* 4.2 3.8 - - - -
65A GLN* 3.0 23.7 + - - +
169A PRO* 2.9 35.1 - - - +
170A LEU* 4.0 9.1 - - - +
173A GLY* 3.5 17.0 - - - +
174A LEU* 4.9 3.1 - - + +
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Residues in contact with THR 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 LEU* 3.4 11.1 + - - +
59A SER* 3.0 12.0 + - - -
61A ALA* 1.3 77.0 - - - +
63A LEU* 1.3 62.5 + - + +
64A ALA 3.0 0.2 - - - -
65A GLN* 2.7 36.6 + - - +
66A SER* 2.9 15.9 + - - +
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Residues in contact with LEU 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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20A ALA* 4.4 17.7 - - + +
23A LEU* 4.4 26.7 - - + -
24A PHE* 3.5 40.2 - - + +
27A ILE* 4.4 9.0 - - + -
59A SER* 3.1 25.7 + - - +
60A ILE* 3.8 5.6 - - - +
62A THR* 1.3 83.4 - - + +
64A ALA* 1.3 57.4 + - - +
66A SER* 3.3 14.2 + - - +
67A VAL* 2.8 29.3 + - + +
73A ALA 4.6 1.5 - - - +
75A LEU* 5.1 6.3 - - + -
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Residues in contact with ALA 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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60A ILE* 2.8 25.9 + - + +
61A ALA* 3.9 6.5 - - - +
63A LEU* 1.3 75.6 - - - +
65A GLN* 1.3 63.0 + - - +
66A SER 3.1 5.6 + - - -
67A VAL* 3.8 19.7 + - - +
73A ALA* 4.2 16.4 - - + +
74A HIS* 6.0 0.4 - - - -
75A LEU* 6.3 0.2 - - + -
162A ARG* 3.6 21.5 + - - +
169A PRO* 4.6 10.1 - - + -
172A ILE* 6.3 4.0 - - + -
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ALA 3.0 17.2 + - - +
62A THR* 2.7 17.2 + - - +
64A ALA* 1.3 76.0 - - - +
66A SER* 1.3 59.7 + - - +
67A VAL 4.8 1.4 - - - +
163A ASP* 4.7 14.2 - - - +
166A GLY* 5.6 8.1 - - - +
169A PRO* 4.2 18.1 - - + +
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Residues in contact with SER 66 (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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62A THR* 2.9 18.9 + - - +
63A LEU* 3.3 17.8 + - - +
65A GLN* 1.3 81.1 - - - +
67A VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 67 (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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16A ALA* 3.8 28.5 - - + +
17A GLU* 6.0 0.7 - - + -
20A ALA* 3.9 13.7 - - + -
63A LEU* 2.8 27.1 - - + +
64A ALA* 3.8 10.9 + - - +
65A GLN 4.8 1.4 - - - +
66A SER* 1.3 82.5 - - - +
68A GLY* 1.3 74.4 + - - +
69A HIS* 3.4 4.5 + - - +
72A GLY 4.1 3.6 - - - +
73A ALA* 3.4 34.8 - - - +
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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