Contacts of the helix formed by residues 62 - 82 (chain A) in PDB entry 3SJ5
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 ASN 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 4.0 2.5 - - - -
60A GLY 3.7 2.8 + - - -
61A LYS* 1.3 74.4 - - - +
63A VAL* 1.3 69.2 + - - +
64A ASN* 2.7 44.4 + - - +
65A GLU* 3.1 33.3 + - + +
66A ILE* 3.2 9.9 + - - +
157B SER* 3.8 31.4 + - - -
158B VAL 5.9 3.9 + - - -
159B GLU* 6.0 1.8 - - - +
177B LYS* 5.6 4.2 - - - +
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG 5.7 0.2 - - - +
52A PHE* 3.7 45.1 - - + +
53A ALA* 4.4 4.0 - - - +
56A SER* 3.6 15.1 + - - -
61A LYS 3.5 1.8 + - - -
62A ASN* 1.3 78.6 - - - +
64A ASN* 1.3 72.4 + - - +
66A ILE* 3.3 6.5 + - + +
67A TRP* 2.9 40.5 + - + +
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 2.7 26.8 + - - +
63A VAL* 1.3 83.2 - - - +
65A GLU* 1.3 53.5 + - - +
67A TRP* 3.4 5.7 + - - -
68A ARG* 3.0 24.1 + - - +
139A ASP* 3.1 42.0 + - - +
158B VAL 5.3 1.4 + - - -
159B GLU* 3.3 44.7 + - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 3.6 31.4 + - - +
62A ASN* 3.1 31.9 + - + +
64A ASN* 1.3 74.1 - - - +
66A ILE* 1.3 67.3 + - - +
68A ARG* 3.3 8.5 + - - +
69A GLU* 3.1 23.2 + - - +
72A ARG* 5.9 0.2 + - - -
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.7 29.6 - - + -
17A TYR* 3.5 24.7 - - + +
52A PHE* 3.9 17.7 - - + +
55A VAL* 4.0 12.8 - - + -
56A SER* 3.8 37.2 - - - +
59A THR* 4.1 5.8 - - - +
61A LYS* 3.8 17.0 - - + +
62A ASN 3.2 7.9 + - - +
63A VAL* 3.3 9.6 + - + +
65A GLU* 1.3 78.6 - - - +
67A TRP* 1.3 61.5 + - - +
69A GLU* 3.2 4.0 + - - +
70A VAL* 2.9 21.5 + - - +
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Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 3.7 34.1 - + - -
48A VAL* 4.0 9.0 - - + -
49A ARG* 5.8 2.8 - - - +
52A PHE* 3.5 54.0 - + + +
63A VAL* 2.9 38.5 + - + +
64A ASN* 3.8 9.0 - - - +
66A ILE* 1.3 76.9 - - - +
68A ARG* 1.3 62.8 + - - +
70A VAL* 3.7 6.5 - - + +
71A GLY 2.9 19.4 + - - -
137A MET* 3.4 31.6 - - + -
139A ASP* 4.0 13.5 - - + -
140A TYR* 3.7 36.8 - + + +
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 3.0 14.6 + - - +
65A GLU* 3.6 11.7 - - - +
66A ILE 3.2 0.2 - - - -
67A TRP* 1.3 76.4 - - - +
69A GLU* 1.3 59.0 + - - +
71A GLY 3.3 0.5 + - - -
72A ARG* 3.0 56.9 + - - +
139A ASP* 3.4 32.5 + - + +
142A LEU* 3.8 36.7 - - - +
143A GLY* 3.4 6.2 - - - -
146A GLU* 3.0 37.5 + - - +
158A VAL* 6.3 0.6 - - - +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.7 32.5 - - + +
17A TYR* 4.5 7.2 - - - +
61A LYS* 5.9 1.8 - - - +
65A GLU 3.1 15.4 + - - +
66A ILE 3.8 3.6 - - - +
68A ARG* 1.3 74.7 - - - +
70A VAL* 1.3 64.5 + - - +
72A ARG* 3.2 32.5 + - - +
73A GLN* 2.8 52.2 + - - +
150A LYS* 4.9 1.9 + - - -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 3.6 37.9 - - + +
12A THR* 4.2 19.3 - - + -
13A LEU* 3.9 28.5 - - + -
16A LEU* 4.5 3.1 - - + -
52A PHE* 4.0 9.6 - - + -
66A ILE* 2.9 21.0 + - + +
67A TRP* 3.3 12.5 + - + +
69A GLU* 1.3 75.9 - - - +
71A GLY* 1.3 63.1 + - - +
73A GLN* 3.2 3.1 + - - +
74A ASN* 3.0 26.2 + - - +
140A TYR* 4.0 9.2 - - + -
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP 2.9 13.2 + - - -
68A ARG 3.7 3.6 - - - -
70A VAL* 1.3 76.5 - - - +
72A ARG* 1.3 61.0 + - - +
74A ASN 3.3 8.1 + - - -
75A ILE* 3.9 2.6 + - - +
140A TYR* 3.6 26.0 - - - -
143A GLY 3.5 6.5 - - - -
144A LEU* 3.3 30.5 - - - +
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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
----------------------------------------------------------
68A ARG* 3.0 42.8 + - - +
69A GLU* 3.2 35.1 + - - +
71A GLY* 1.3 77.1 - - - +
73A GLN* 1.3 64.1 + - - +
75A ILE* 4.1 5.4 + - - +
76A LYS* 5.0 6.9 + - - +
143A GLY* 3.3 19.3 + - - +
146A GLU* 2.7 36.8 + - + +
147A GLY* 3.6 17.5 - - - +
150A LYS* 3.7 31.2 + - - +
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.8 25.1 - - + +
16A LEU* 4.5 12.4 - - + +
69A GLU* 2.8 40.9 + - - +
70A VAL 3.8 3.4 - - - +
72A ARG* 1.3 80.7 + - - +
74A ASN* 1.3 65.2 + - - +
75A ILE 3.3 1.4 + - - -
76A LYS* 3.0 53.4 + - - +
77A THR* 4.0 5.4 + - - -
150A LYS* 4.9 6.1 - - - +
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 4.4 0.5 - - - -
8A THR* 3.7 19.2 - - - +
9A TRP* 3.2 26.1 + - - -
12A THR* 4.0 10.5 + - - -
70A VAL* 3.0 18.7 + - - +
71A GLY* 3.3 7.9 + - - +
73A GLN* 1.3 77.3 - - - +
75A ILE* 1.3 65.1 + - - +
77A THR* 3.0 16.5 + - - -
78A PHE* 3.0 33.9 + - + -
140A TYR* 2.7 25.2 + - - +
144A LEU* 3.9 11.2 - - + -
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY 4.1 4.7 - - - +
72A ARG 4.5 2.7 - - - +
73A GLN 3.3 1.4 - - - -
74A ASN* 1.3 75.9 - - - +
76A LYS* 1.3 63.7 + - + +
78A PHE* 3.2 8.9 + - + +
79A SER* 3.1 18.5 + - - -
86A PHE* 3.8 25.6 - - + -
94A PHE* 4.8 3.4 - - + -
144A LEU* 3.5 42.6 - - + +
147A GLY 3.9 10.3 - - - +
148A SER* 3.4 27.1 - - - +
151A PHE* 4.1 21.5 - - + -
500A HEM 4.0 22.2 - - + -
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Residues in contact with LYS 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 5.0 4.5 - - - +
73A GLN* 3.0 45.7 + - - +
74A ASN 3.2 0.2 - - - -
75A ILE* 1.3 78.8 - - + +
77A THR* 1.3 62.5 + - - +
79A SER* 2.8 25.7 + - - -
80A GLU* 3.3 12.6 + - - +
150A LYS* 6.5 2.5 - - - -
151A PHE* 4.1 20.0 - - + -
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Residues in contact with THR 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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8A THR* 3.5 27.9 - - + +
12A THR* 5.2 2.1 + - - -
73A GLN 4.1 7.8 + - - -
74A ASN* 3.0 11.3 + - - -
76A LYS* 1.3 79.9 - - - +
78A PHE* 1.3 64.3 + - - +
80A GLU* 3.0 35.4 + - - +
81A TRP* 3.3 41.5 + - + +
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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
----------------------------------------------------------
5A PHE* 3.7 25.8 - + - -
8A THR* 5.5 1.8 - - + -
74A ASN* 3.0 41.6 + - - -
75A ILE* 3.2 12.8 + - + +
77A THR* 1.3 80.5 - - - +
79A SER* 1.3 56.9 + - - +
81A TRP* 3.1 23.4 + + - +
82A PHE* 2.8 38.8 + + + +
86A PHE* 3.8 3.4 - - + -
140A TYR* 3.7 8.3 - - - -
144A LEU* 3.8 22.0 - - + -
500A HEM 3.6 59.5 - + + -
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE 3.1 6.2 + - - -
76A LYS* 2.8 17.9 + - - -
78A PHE* 1.3 76.7 - - - +
80A GLU* 1.3 60.9 + - - +
82A PHE 4.2 0.4 - - - +
83A PRO* 3.6 23.4 - - - +
86A PHE* 3.4 27.3 - - - -
151A PHE* 3.3 38.0 - - - -
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 3.5 12.3 - - - +
77A THR* 3.0 30.6 + - - +
79A SER* 1.3 81.3 + - - +
81A TRP* 1.3 73.3 + - + +
83A PRO* 3.8 7.4 - - - +
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Residues in contact with TRP 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 4.3 24.9 - - + -
5A PHE* 5.5 7.4 - + - -
8A THR* 2.7 30.5 - - + -
77A THR* 3.5 28.4 - - + +
78A PHE* 3.1 26.6 + + - +
80A GLU* 1.3 92.3 + - + +
82A PHE* 1.3 93.2 + + + +
83A PRO* 3.4 8.1 - - - +
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 6.5 0.7 - + - -
78A PHE* 2.8 25.3 + + - +
79A SER 4.2 0.2 - - - -
81A TRP* 1.3 108.8 - + + +
83A PRO* 1.3 64.4 - - - +
84A SER* 3.1 6.0 + - - +
85A TYR* 3.2 41.6 + + + +
86A PHE* 3.4 12.4 - - - -
105A LEU* 3.9 30.7 - - + -
500A HEM 3.7 23.3 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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