Contacts of the helix formed by residues 61 - 81 (chain A) in PDB entry 2JFS
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PHE* 4.0 0.5 - - - -
59A ALA* 2.9 13.6 + - - +
60A PRO* 1.3 74.8 - - - +
62A ARG* 1.3 60.1 + - - +
63A ASP* 3.6 8.6 + - - +
64A GLY* 2.8 34.7 + - - -
65A LEU* 2.8 29.1 + - - +
97A PHE* 3.4 14.1 - - - -
101A GLN* 3.5 20.2 - - + +
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Residues in contact with ARG 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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61A ASP* 1.3 75.3 - - - +
63A ASP* 1.3 72.4 + - - +
65A LEU* 3.3 2.7 + - - +
66A LEU* 3.1 44.2 + - + +
97A PHE* 3.6 15.7 - - + -
101A GLN* 4.7 13.2 + - - +
105A LEU* 3.5 33.8 - - + +
169A VAL* 3.6 25.4 + - - +
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Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 3.3 9.5 + - - +
62A ARG* 1.3 93.1 + - - +
64A GLY* 1.3 58.1 + - - +
66A LEU* 3.5 7.4 + - - +
67A GLU* 3.0 30.8 + - - +
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Residues in contact with GLY 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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55A GLY 4.4 4.6 - - - +
56A PHE* 4.8 0.9 - - - -
59A ALA* 3.1 36.1 - - - -
61A ASP* 2.8 16.7 + - - -
63A ASP* 1.3 72.8 - - - +
65A LEU* 1.3 57.1 + - - +
67A GLU* 3.8 4.5 - - - +
68A ALA* 2.9 29.5 + - - +
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Residues in contact with LEU 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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30A LEU* 4.0 15.0 - - + -
52A LEU* 4.0 21.8 - - + -
56A PHE* 3.9 24.4 - - + -
59A ALA 4.0 0.6 + - - -
61A ASP 2.8 12.3 + - - +
62A ARG* 3.5 9.6 - - - +
64A GLY* 1.3 74.1 - - - +
66A LEU* 1.3 60.0 + - - +
68A ALA* 3.2 5.0 + - - +
69A VAL* 3.0 32.1 + - + +
93A ALA* 4.8 6.5 - - + -
94A VAL 5.4 0.7 - - - -
95A ALA* 3.9 26.9 - - + +
97A PHE* 4.4 0.7 - - + -
105A LEU* 3.9 19.1 - - + +
107A VAL* 3.8 25.8 - - + -
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Residues in contact with LEU 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 ARG* 3.1 56.5 + - + +
63A ASP* 3.9 8.3 - - - +
65A LEU* 1.3 79.4 - - + +
67A GLU* 1.3 62.1 + - - +
69A VAL* 3.3 7.7 + - + +
70A GLN* 3.1 26.6 + - - +
105A LEU* 5.1 0.7 - - + -
107A VAL* 3.9 17.7 - - + -
167A PRO* 5.4 3.1 - - + -
169A VAL* 3.2 39.0 - - + -
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Residues in contact with GLU 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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63A ASP 3.0 18.6 + - - +
64A GLY* 3.9 6.1 - - - +
66A LEU* 1.3 75.8 - - - +
68A ALA* 1.3 58.3 + - - +
70A GLN* 3.1 18.1 + - - +
71A GLN* 2.8 41.8 + - + +
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Residues in contact with ALA 68 (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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51A THR* 4.4 1.7 - - - +
52A LEU* 3.7 36.4 - - + +
55A GLY* 3.9 10.1 - - - -
56A PHE* 3.8 11.7 - - + +
64A GLY 2.9 19.2 + - - +
65A LEU* 3.2 7.2 + - - +
67A GLU* 1.3 75.2 - - - +
69A VAL* 1.3 58.0 + - - +
71A GLN* 3.3 8.0 + - - +
72A ALA* 2.8 29.5 + - - +
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Residues in contact with VAL 69 (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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52A LEU* 3.7 19.1 - - + -
65A LEU* 3.0 22.9 + - + +
66A LEU* 3.5 9.2 - - + +
68A ALA* 1.3 72.0 - - - +
70A GLN* 1.3 67.5 + - - +
72A ALA* 3.3 6.7 + - - +
73A ASN* 3.1 21.3 + - - +
91A LEU* 4.2 10.5 - - + -
93A ALA* 5.5 1.8 - - + -
107A VAL* 3.9 26.2 - - + -
109A ILE* 5.6 2.2 - - + -
159A LEU* 4.0 10.2 - - + +
165A ILE* 3.9 19.5 - - + -
167A PRO* 4.3 18.4 - - + -
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Residues in contact with GLN 70 (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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66A LEU 3.1 14.5 + - - +
67A GLU* 3.1 23.4 + - - +
69A VAL* 1.3 76.4 - - - +
71A GLN* 1.3 61.4 + - - +
73A ASN* 3.3 7.2 + - - +
74A LEU* 3.1 28.1 + - + +
163A PRO 5.0 5.9 - - - +
165A ILE* 3.3 43.4 + - - +
167A PRO* 3.9 14.8 - - - +
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Residues in contact with GLN 71 (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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51A THR* 3.6 13.5 - - + +
55A GLY* 6.4 0.9 - - - -
67A GLU* 2.8 31.9 + - + +
68A ALA* 3.3 7.4 + - - +
70A GLN* 1.3 69.6 - - - +
72A ALA* 1.3 60.9 - - - +
74A LEU* 3.2 31.2 - - - +
75A ARG* 2.9 31.9 + - - +
78A GLU* 5.1 2.8 - - - +
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Residues in contact with ALA 72 (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 ALA* 3.5 32.1 - - + +
51A THR* 3.5 14.7 - - - +
52A LEU* 4.4 1.8 - - - +
68A ALA 2.8 17.4 + - - +
69A VAL* 3.3 8.7 + - - +
71A GLN* 1.3 76.8 + - - +
73A ASN* 1.3 62.7 + - - +
75A ARG* 3.9 0.5 - - - +
76A VAL* 3.0 29.5 + - - +
91A LEU* 4.8 3.8 - - + -
159A LEU* 3.9 11.7 - - + -
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Residues in contact with ASN 73 (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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69A VAL 3.1 7.0 + - - +
70A GLN* 3.5 10.5 + - - +
71A GLN 3.3 0.2 - - - +
72A ALA* 1.3 77.1 - - - +
74A LEU* 1.3 66.8 + - - +
77A PHE* 3.0 22.9 + - - +
159A LEU* 3.7 12.0 - - + +
160A GLY* 2.7 28.8 + - - -
162A GLY 2.9 25.9 + - - +
163A PRO* 3.5 20.2 + - - +
165A ILE* 3.1 47.4 - - + +
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Residues in contact with LEU 74 (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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70A GLN* 3.1 14.6 + - + +
71A GLN* 3.2 33.0 - - - +
73A ASN* 1.3 82.1 - - - +
75A ARG* 1.3 58.3 + - - +
77A PHE* 3.8 7.1 - - + +
78A GLU* 2.9 50.0 + - + +
163A PRO* 3.9 35.7 - - + +
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Residues in contact with ARG 75 (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 THR* 3.6 11.4 - - + -
51A THR* 3.8 18.2 - - + +
71A GLN* 2.9 22.4 + - - +
72A ALA 4.0 1.6 - - - +
74A LEU* 1.3 76.0 - - - +
76A VAL* 1.3 64.1 - - - +
78A GLU* 3.4 25.6 + - - +
79A LEU* 3.1 41.1 - - - +
1240A GOL 2.6 59.0 + - - +
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Residues in contact with VAL 76 (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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44A ALA* 3.5 47.8 - - + +
47A THR* 3.9 11.9 - - + -
48A ALA* 3.7 14.1 - - - +
72A ALA 3.0 17.6 + - - +
75A ARG* 1.3 75.6 + - - +
77A PHE* 1.3 56.8 + - - +
79A LEU* 3.3 4.0 + - + +
80A LEU* 2.8 36.7 + - + +
88A GLY* 4.8 1.3 - - - -
159A LEU* 4.0 12.1 - - + +
160A GLY* 3.7 24.5 - - - +
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Residues in contact with PHE 77 (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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73A ASN 3.0 19.3 + - - +
74A LEU* 3.8 8.7 - - + +
76A VAL* 1.3 74.5 - - - +
78A GLU* 1.3 67.6 + - + +
81A GLY* 2.8 51.1 + - - +
160A GLY 3.4 13.4 + - - +
161A ILE* 3.4 33.4 - - - -
162A GLY* 4.0 17.7 - - - +
163A PRO* 4.0 24.2 - - + -
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Residues in contact with GLU 78 (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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71A GLN* 5.1 2.4 - - - +
74A LEU* 2.9 40.0 + - + +
75A ARG* 4.0 26.7 + - - +
77A PHE* 1.3 85.6 - - + +
79A LEU* 1.3 61.8 + - - +
81A GLY 4.5 1.0 + - - -
82A ASP* 5.0 7.6 + - - +
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Residues in contact with LEU 79 (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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40A ARG* 4.6 16.3 + - - +
43A HIS* 4.5 11.9 - - + +
47A THR* 3.7 30.5 - - + +
75A ARG* 3.1 36.0 - - - +
76A VAL* 3.7 3.1 - - - +
78A GLU* 1.3 81.2 - - - +
80A LEU* 1.3 83.3 + - + +
82A ASP* 5.2 0.9 + - - +
83A GLU* 4.8 2.4 - - - +
1240A GOL 4.6 9.4 - - - +
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Residues in contact with LEU 80 (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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40A ARG* 3.4 60.8 - - + +
43A HIS* 4.6 2.5 - - + -
44A ALA* 3.7 36.1 - - + +
76A VAL* 2.8 23.3 + - + +
79A LEU* 1.3 87.2 - - + +
81A GLY* 1.3 64.6 + - - +
82A ASP 3.2 2.9 - - - -
83A GLU* 3.1 27.7 + - + +
85A THR 4.7 2.9 - - - +
86A VAL* 6.0 0.2 - - - -
87A SER* 4.1 26.6 + - - +
160A GLY 5.3 1.6 - - - +
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Residues in contact with GLY 81 (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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77A PHE* 2.8 49.5 + - - +
78A GLU 4.5 0.6 + - - -
79A LEU 3.7 0.6 - - - -
80A LEU* 1.3 71.5 - - - +
82A ASP* 1.3 63.8 + - - +
83A GLU 3.4 4.8 + - - +
160A GLY 5.3 1.6 - - - -
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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
------------------------------------------------------------
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