Contacts of the helix formed by residues 48 - 66 (chain A) in PDB entry 1PF5
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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46A GLU* 3.2 17.8 + - - +
47A PRO* 1.3 78.0 - - - +
49A PHE* 1.3 63.1 + - - +
50A GLN* 3.7 9.8 + - - +
51A GLN* 3.1 33.7 + - + +
52A GLN 2.9 23.9 + - - -
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Residues in contact with PHE 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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47A PRO 3.4 4.9 + - - -
48A ASP* 1.3 74.9 + - - +
50A GLN* 1.3 58.1 + - - +
52A GLN* 2.7 33.6 + - + +
53A VAL* 2.9 35.2 + - + +
86A ASN 5.4 0.4 - - - -
87A GLN* 3.3 54.3 - - + -
90A ASP* 3.8 21.3 - - + +
91A ILE* 3.8 11.7 - - + -
119A ASP* 3.7 38.8 - - + -
120A PHE* 4.0 7.4 - - + -
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Residues in contact with GLN 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* 3.6 10.0 + - - +
49A PHE* 1.3 81.6 - - - +
51A GLN* 1.3 60.3 + - - +
53A VAL* 3.5 7.5 + - - +
54A ARG* 2.7 68.6 + - - +
90A ASP* 3.1 30.1 + - - +
93A THR* 4.2 14.1 + - - +
94A VAL* 3.8 14.8 - - + -
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Residues in contact with GLN 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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46A GLU* 3.2 29.0 - - + +
48A ASP* 3.1 28.5 + - + +
49A PHE 3.0 0.6 - - - -
50A GLN* 1.3 76.6 + - - +
52A GLN* 1.3 61.5 + - - +
54A ARG* 3.3 26.3 + - - +
55A LEU* 2.9 30.7 + - - +
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Residues in contact with GLN 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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38A GLY* 3.2 30.4 - - - +
45A PRO* 3.8 9.6 - - - +
46A GLU* 3.3 31.4 - - - +
47A PRO 5.2 1.2 - - - +
48A ASP 2.9 6.5 + - - +
49A PHE* 2.7 21.7 + - + +
51A GLN* 1.3 72.1 - - - +
53A VAL* 1.3 56.1 + - - +
55A LEU 3.3 0.3 + - - -
56A ALA* 2.8 26.6 + - + +
117A GLY 5.1 0.2 - - - +
118A PHE* 3.5 19.3 - - - +
119A ASP* 2.9 44.8 + - - +
120A PHE* 3.4 19.1 + - + +
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Residues in contact with VAL 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 PHE* 2.9 50.7 + - + +
50A GLN* 3.7 8.1 - - - +
52A GLN* 1.3 77.0 - - - +
54A ARG* 1.3 61.9 + - - +
56A ALA* 3.3 7.1 + - - +
57A PHE* 3.0 51.5 + - + -
91A ILE* 4.4 11.7 - - + -
94A VAL* 3.9 20.2 - - + -
120A PHE* 4.1 25.4 - - + -
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Residues in contact with ARG 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 GLN* 2.7 50.2 + - - +
51A GLN* 3.5 27.9 + - - +
53A VAL* 1.3 73.7 - - - +
55A LEU* 1.3 60.6 + - - +
57A PHE* 3.2 6.0 + - - +
58A ASP* 2.9 34.7 + - - +
93A THR* 3.8 12.1 - - - +
94A VAL* 3.8 25.9 - - + +
97A GLU* 2.7 43.2 + - - -
98A ILE* 6.1 0.2 - - - -
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Residues in contact with LEU 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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38A GLY* 3.6 15.5 - - - +
39A SER 3.4 22.7 - - - +
40A ARG* 4.1 9.2 - - + +
46A GLU* 4.1 18.6 - - + -
51A GLN 2.9 17.7 + - - +
52A GLN* 3.7 4.3 - - - +
54A ARG* 1.3 73.6 - - - +
56A ALA* 1.3 54.9 + - - +
58A ASP* 3.0 15.3 + - + +
59A ASN* 2.7 58.1 + - - +
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Residues in contact with ALA 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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36A GLN* 3.9 8.2 - - - +
37A VAL* 3.6 19.7 - - - -
38A GLY* 3.4 12.8 - - - +
52A GLN 2.8 14.9 + - - +
53A VAL 3.4 9.6 - - - +
55A LEU* 1.3 76.5 - - - +
57A PHE* 1.3 56.3 + - - +
59A ASN* 3.3 3.1 + - - +
60A LEU* 2.8 28.8 + - - +
120A PHE* 3.7 27.4 - - + -
122A ILE* 5.1 2.2 - - + -
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Residues in contact with PHE 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 VAL* 3.0 44.8 + - + -
54A ARG* 3.2 8.5 + - - +
56A ALA* 1.3 72.9 - - - +
58A ASP* 1.3 63.4 + - - +
60A LEU* 3.3 13.4 + - + +
61A HIS* 2.9 29.3 + - - +
71A PHE* 3.5 16.3 - + + -
91A ILE* 5.5 2.9 - - + -
94A VAL* 3.9 11.7 - - + -
95A LYS* 4.9 9.4 - - + -
98A ILE* 3.2 35.4 - - + -
99A PHE* 4.1 18.6 - + - -
107A TRP* 4.4 11.9 - + - -
120A PHE* 3.9 14.1 - + - -
122A ILE* 3.9 29.4 - - + -
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Residues in contact with ASP 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 ARG* 2.9 20.9 + - - +
55A LEU* 3.0 22.6 + - + +
57A PHE* 1.3 76.4 - - - +
59A ASN* 1.3 65.8 + - - +
61A HIS* 3.3 7.2 + - - +
62A ALA* 3.0 24.1 + - - +
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Residues in contact with ASN 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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9A PRO* 4.7 2.4 - - + +
13A HIS* 4.6 17.4 + - - -
36A GLN* 3.6 14.1 - - - +
37A VAL 2.8 26.1 + - - +
39A SER* 3.3 29.7 + - - +
55A LEU* 2.7 32.5 + - - +
56A ALA 3.6 4.5 - - - +
58A ASP* 1.3 72.6 - - - +
60A LEU* 1.3 62.9 + - - +
62A ALA* 3.3 8.0 + - - +
63A THR* 3.0 27.5 + - - -
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Residues in contact with LEU 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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33A VAL* 4.1 16.6 - - + -
36A GLN* 3.7 26.2 + - + -
56A ALA 2.8 17.5 + - - +
57A PHE* 3.5 13.9 - - + +
58A ASP 3.2 0.2 - - - -
59A ASN* 1.3 76.9 - - - +
61A HIS* 1.3 58.2 + - - +
63A THR* 3.1 3.3 + - - -
64A LEU* 2.9 39.1 + - + +
71A PHE* 4.0 19.3 - - + -
74A ILE* 4.3 15.0 - - + -
122A ILE* 4.2 25.8 - - + +
124A VAL* 4.3 19.5 - - + -
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Residues in contact with HIS 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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57A PHE 2.9 17.6 + - - +
58A ASP* 3.6 7.2 - - - +
60A LEU* 1.3 75.7 - - - +
62A ALA* 1.3 57.6 + - - +
64A LEU* 3.2 5.2 + - - +
65A ALA* 2.8 39.5 + - + +
69A CYS 5.4 1.6 - - - -
70A THR* 4.5 20.4 - - + +
71A PHE* 3.6 45.5 + + + -
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Residues in contact with ALA 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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9A PRO* 3.8 19.9 - - + +
10A ALA 4.5 5.0 + - - +
13A HIS* 5.8 3.6 - - + +
58A ASP 3.0 16.2 + - - +
59A ASN* 3.6 8.3 - - - +
60A LEU 3.2 0.2 - - - -
61A HIS* 1.3 77.1 - - - +
63A THR* 1.3 62.8 + - - +
65A ALA* 3.5 8.5 + - - +
66A ALA* 3.2 20.4 + - - +
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Residues in contact with THR 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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7A VAL* 3.8 7.6 - - + +
9A PRO* 3.1 23.1 - - + +
16A TYR* 4.2 0.5 + - - -
23A ALA* 3.7 28.9 - - + +
24A ALA* 3.9 20.6 - - + -
31A LEU* 5.1 1.5 - - + +
33A VAL* 4.0 11.2 - - + -
36A GLN* 3.3 16.1 + - - +
59A ASN 3.0 15.2 + - - -
60A LEU 3.1 7.4 + - - -
62A ALA* 1.3 73.4 - - - +
64A LEU* 1.3 67.6 + - - +
66A ALA* 3.2 16.6 + - - +
67A ALA* 3.7 3.5 + - - +
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Residues in contact with LEU 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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31A LEU* 4.0 19.1 - - + -
33A VAL* 4.3 11.4 - - + -
60A LEU* 2.9 22.0 + - + +
61A HIS* 3.5 7.0 - - - +
63A THR* 1.3 76.8 - - - +
65A ALA* 1.3 64.6 + - - +
67A ALA* 2.9 10.6 + - - +
69A CYS* 2.9 47.0 + - + +
70A THR* 3.6 16.4 - - - +
71A PHE* 3.6 35.7 - - + +
74A ILE* 4.1 10.8 - - + -
124A VAL* 4.8 3.4 - - + -
126A ALA* 4.1 15.0 - - + -
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Residues in contact with ALA 65 (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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61A HIS* 2.8 29.9 + - + +
62A ALA* 3.5 9.9 - - - +
63A THR 3.3 0.2 - - - -
64A LEU* 1.3 71.3 - - - +
66A ALA* 1.3 56.6 + - - +
68A GLY* 2.7 23.7 + - - +
69A CYS 3.4 11.6 + - - +
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Residues in contact with ALA 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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7A VAL* 3.5 15.0 - - + +
8A PHE 2.9 31.4 - - - +
9A PRO* 4.2 2.0 - - + -
10A ALA* 4.8 3.1 - - + +
62A ALA 3.2 7.1 + - - +
63A THR 3.2 13.4 + - - +
64A LEU 3.2 0.6 - - - -
65A ALA* 1.3 77.5 - - - +
67A ALA* 1.3 56.0 + - - +
68A GLY 3.4 0.2 - - - -
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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