Contacts of the helix formed by residues 69 - 84 (chain A) in PDB entry 1SLY
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 PRO 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TYR* 4.9 1.3 - - - +
67A THR 3.2 8.7 - - - +
68A LEU* 1.3 81.4 - - - +
70A PRO* 1.4 67.3 - - + +
71A ALA 3.2 0.5 + - - -
72A ARG* 3.3 26.1 + - - +
73A THR* 3.7 7.6 + - - -
399A THR* 6.5 0.2 - - + -
402A SER* 3.8 28.0 - - - +
403A GLU* 3.4 26.2 - - - +
406A ASN* 3.2 25.1 - - - +
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Residues in contact with PRO 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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40A TYR* 3.5 30.7 - - + +
43A TYR* 3.4 45.1 - - + -
68A LEU* 3.5 20.2 - - + -
69A PRO* 1.4 89.3 - - + +
71A ALA* 1.3 57.0 + - - -
72A ARG 3.3 0.4 - - - -
73A THR* 3.6 10.3 + - - +
74A LEU* 3.0 22.5 + - - +
399A THR* 6.1 0.4 - - + -
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Residues in contact with ALA 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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61A PHE* 4.3 12.3 - - + -
62A VAL* 3.9 21.7 - - + +
65A ASN* 3.2 31.9 - - + +
68A LEU* 2.9 18.0 + - + +
70A PRO* 1.3 76.0 - - - +
72A ARG* 1.3 65.5 + - + +
74A LEU* 3.3 7.4 + - - +
75A GLN* 3.2 22.9 + - - +
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Residues in contact with ARG 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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62A VAL* 6.3 0.2 - - + -
66A PRO 2.8 30.2 + - - +
67A THR* 3.4 22.6 + - - +
68A LEU 4.0 5.9 + - - +
69A PRO* 3.3 14.8 + - - +
70A PRO 3.3 0.4 - - - -
71A ALA* 1.3 75.3 - - + +
73A THR* 1.3 65.3 + - - +
75A GLN* 3.2 27.1 + - - +
76A SER* 3.5 13.9 + - - -
406A ASN* 2.8 34.6 + - - +
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Residues in contact with THR 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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43A TYR* 4.0 15.9 - - - +
69A PRO 3.7 7.6 + - - -
70A PRO* 3.6 14.5 + - - +
71A ALA 3.5 0.2 - - - -
72A ARG* 1.3 77.2 - - - +
74A LEU* 1.4 56.8 + - - +
76A SER* 3.5 6.9 + - - -
77A ARG* 2.9 43.0 + - + +
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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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43A TYR* 3.4 27.5 - - + -
46A ILE* 4.0 17.3 - - + -
47A THR* 4.0 14.8 - - + -
50A LEU* 4.1 21.5 - - + -
58A VAL* 4.0 21.8 - - + -
61A PHE* 3.8 26.0 - - + -
62A VAL* 4.5 5.4 - - + -
70A PRO 3.0 11.0 + - - +
71A ALA 3.3 10.5 + - - +
73A THR* 1.4 72.0 - - - +
75A GLN* 1.3 56.6 + - - +
77A ARG* 3.0 11.1 + - + +
78A PHE* 2.7 38.5 + - - +
94A PHE* 5.2 0.4 - - - -
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Residues in contact with GLN 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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62A VAL* 3.5 31.4 - - + +
71A ALA 3.2 12.1 + - - +
72A ARG* 3.2 19.3 + - - +
74A LEU* 1.3 73.9 - - - +
76A SER* 1.3 60.6 + - - +
79A VAL* 2.9 37.2 + - + +
94A PHE* 3.6 23.4 - - + +
95A SER* 4.6 11.7 + - - +
99A PRO* 5.6 5.2 - - + +
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Residues in contact with SER 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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72A ARG 3.5 9.4 + - - -
73A THR* 3.9 8.1 - - - -
74A LEU 3.3 0.6 - - - -
75A GLN* 1.3 79.7 - - - +
77A ARG* 1.3 59.8 + - - +
79A VAL* 3.7 4.1 - - - +
80A ASN* 2.8 31.5 + - - -
99A PRO* 4.1 2.9 - - - +
100A GLY* 3.7 11.3 + - - -
101A THR* 3.6 40.9 + - - -
104A ALA* 4.1 9.5 - - - +
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Residues in contact with ARG 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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43A TYR* 2.7 31.6 + - - -
47A THR* 3.7 29.5 + - - +
50A LEU* 4.3 19.7 - - + +
73A THR* 2.9 32.1 + - + +
74A LEU* 3.5 12.3 - - + +
76A SER* 1.3 77.1 - - - +
78A PHE* 1.3 64.2 + - - +
80A ASN* 3.4 11.2 + - + +
81A GLU* 3.1 18.9 + - - +
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Residues in contact with PHE 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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50A LEU* 4.0 17.9 - - + +
53A GLN* 3.7 18.8 - - + -
55A ALA* 3.6 29.2 - - + -
58A VAL* 3.9 28.3 - - + -
74A LEU* 2.7 20.7 + - + +
77A ARG* 1.3 72.5 - - - +
79A VAL* 1.3 63.5 + - - +
81A GLU* 2.8 27.0 + - + +
82A LEU* 2.9 43.6 + - + +
85A ARG* 3.7 20.6 - - - -
94A PHE* 3.6 30.3 - + + -
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Residues in contact with VAL 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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75A GLN 2.9 24.5 + - - +
76A SER* 3.7 7.2 - - - +
78A PHE* 1.3 74.0 - - - +
80A ASN* 1.3 62.0 + - - +
82A LEU* 3.4 2.3 + - - -
83A ALA* 3.0 19.4 + - - +
91A LEU* 3.4 33.6 - - + +
94A PHE* 4.0 9.4 - - + -
95A SER* 3.5 32.5 - - - +
99A PRO* 4.2 11.4 - - + -
104A ALA* 3.8 26.9 - - - +
107A ASN* 4.4 2.5 - - + -
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Residues in contact with ASN 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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76A SER 2.8 22.5 + - - -
77A ARG* 3.4 10.8 + - - +
78A PHE 3.3 0.4 - - - -
79A VAL* 1.3 74.9 - - - +
81A GLU* 1.4 57.2 + - - +
83A ALA* 3.1 10.3 - - - +
84A ARG* 2.9 26.0 + - - +
101A THR* 4.5 4.8 - - - +
103A GLU* 3.5 38.5 + - - +
104A ALA* 3.6 5.9 + - - +
107A ASN* 2.9 25.8 + - - +
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Residues in contact with GLU 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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50A LEU* 3.9 17.6 - - + +
51A MET* 3.5 19.0 + - - +
77A ARG 3.1 11.9 + - - +
78A PHE* 2.8 26.7 + - + +
80A ASN* 1.4 67.3 - - - +
82A LEU* 1.3 58.3 + - - +
84A ARG* 2.6 51.2 + - - +
85A ARG* 2.9 68.9 + - - +
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Residues in contact with LEU 82 (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 ALA* 4.9 7.6 - - + -
78A PHE* 2.9 52.6 + - + +
79A VAL* 3.7 7.0 - - - +
81A GLU* 1.3 70.0 - - - +
83A ALA* 1.3 56.8 + - - +
85A ARG* 3.3 20.6 + - - +
86A GLU 2.9 7.4 + - - -
87A ASP* 2.9 48.2 + - - +
90A GLY 3.8 2.7 - - - +
91A LEU* 3.6 39.5 - - + +
94A PHE* 3.8 23.8 - - + -
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Residues in contact with ALA 83 (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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79A VAL 3.0 13.6 + - - +
80A ASN 3.1 13.9 - - - +
82A LEU* 1.3 75.7 - - - +
84A ARG* 1.3 53.7 + - - +
86A GLU* 3.0 17.2 + - - +
88A TRP* 3.4 33.7 - - + -
91A LEU* 3.8 3.0 - - + +
107A ASN* 3.5 35.2 - - + +
141A LYS* 5.8 1.0 - - - -
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Residues in contact with ARG 84 (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 MET* 3.4 48.5 + - - +
80A ASN 2.9 14.5 + - - +
81A GLU* 2.6 48.1 + - - +
83A ALA* 1.3 71.0 - - - +
85A ARG* 1.3 72.5 + - - +
86A GLU* 3.4 7.4 + - - +
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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