Contacts of the helix formed by residues 71 - 88 (chain A) in PDB entry 3E61
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GOL 3.0 34.2 + - - -
68A ASP* 3.1 28.4 + - - +
69A MET 4.6 1.3 - - - -
70A SER* 1.3 77.6 - - - +
72A PRO* 1.4 70.9 - - - +
73A PHE* 3.1 20.9 + - - +
74A PHE* 2.9 28.6 + - + +
75A THR* 3.2 10.2 + - - +
188A PHE* 5.4 0.6 - - - -
236A ASN* 3.6 9.8 + - - +
238A LEU* 3.7 16.2 - - + +
264A ASP* 4.5 1.2 - - - +
266A ILE* 4.7 2.3 - - - +
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Residues in contact with PRO 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER 3.4 10.5 - - - +
71A ASN* 1.4 88.7 - - - +
73A PHE* 1.3 61.2 + - - +
75A THR* 3.0 23.7 + - + +
76A LEU* 3.0 16.6 + - - +
238A LEU* 3.9 15.7 - - + -
266A ILE* 4.0 22.4 - - + -
267A PRO* 5.0 8.2 - - + +
268A PHE* 3.8 32.8 - - + -
70B SER* 4.9 12.1 - - - +
72B PRO* 5.8 1.8 - - + -
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Residues in contact with PHE 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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1A GOL 3.3 35.4 - - - -
71A ASN* 3.0 14.9 + - - +
72A PRO* 1.3 78.5 - - - +
74A PHE* 1.3 70.7 + + - +
76A LEU* 3.4 5.9 + - - +
77A ILE* 3.1 49.1 + - + +
264A ASP* 3.5 30.5 - - + +
266A ILE* 3.5 11.6 - - + +
281A GLN* 3.4 39.9 - - + -
283A ALA* 3.7 26.4 - - + +
286A LEU* 3.9 9.0 - - + -
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Residues in contact with PHE 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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1A GOL 3.8 29.6 - - - -
66A LEU* 3.8 19.7 - - + +
67A PRO* 3.5 40.4 - - + -
68A ASP* 3.8 26.0 - - + +
71A ASN* 2.9 19.9 + - + +
73A PHE* 1.3 92.4 - + - +
75A THR* 1.3 60.4 + - - +
77A ILE* 3.4 21.7 + - + +
78A ALA* 3.0 27.9 + - - +
122A THR* 4.5 10.8 - - + -
143A ILE* 4.6 7.2 - - + -
188A PHE* 5.9 1.6 - + - -
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Residues in contact with THR 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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66A LEU* 4.7 1.1 - - + -
69A MET* 3.2 30.5 - - - +
71A ASN 3.2 7.1 + - - +
72A PRO* 3.0 23.4 + - - +
74A PHE* 1.3 76.0 - - - +
76A LEU* 1.3 55.6 + - - +
78A ALA* 3.4 9.2 + - - +
79A ARG* 3.1 24.9 + - - +
69B MET* 3.3 46.3 - - + +
70B SER* 3.9 15.7 - - - -
96B ASN* 5.6 1.6 + - - -
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Residues in contact with LEU 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 PRO 3.0 18.2 + - - +
73A PHE* 3.5 4.9 - - - +
75A THR* 1.3 74.2 + - - +
77A ILE* 1.3 66.2 + - - +
78A ALA 3.1 0.9 - - - -
79A ARG* 3.2 16.3 + - + +
80A GLY 3.1 17.5 + - - -
265A ASN 5.7 4.0 - - - +
266A ILE* 5.9 2.7 - - + -
267A PRO* 5.2 15.9 - - + -
283A ALA* 3.7 22.2 - - + +
284A TYR* 3.8 35.5 - - + +
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Residues in contact with ILE 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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64A LEU* 5.1 4.5 - - + -
66A LEU* 5.3 0.9 - - + -
73A PHE* 3.1 44.3 + - + +
74A PHE* 3.4 26.0 + - + +
76A LEU* 1.3 72.8 - - - +
78A ALA* 1.3 58.5 + - - +
80A GLY 3.1 2.9 + - - -
81A VAL* 3.0 30.2 + - + +
143A ILE* 3.9 34.1 - - + -
283A ALA* 3.5 25.9 + - + +
286A LEU* 4.2 12.3 - - + -
287A GLY* 3.4 19.3 - - - +
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Residues in contact with ALA 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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64A LEU* 3.8 27.3 - - + +
66A LEU* 4.2 6.7 - - + -
74A PHE 3.0 14.2 + - - +
75A THR* 3.4 11.9 - - - +
76A LEU 3.1 0.4 - - - -
77A ILE* 1.3 76.2 - - - +
79A ARG* 1.3 57.6 + - - +
81A VAL* 3.5 2.5 + - - +
82A GLU* 2.9 36.3 + - - +
94A ILE* 4.9 0.2 - - + -
69B MET* 3.6 24.5 - - + -
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Residues in contact with ARG 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 THR 3.1 13.3 + - - +
76A LEU* 3.2 20.3 + - - +
78A ALA* 1.3 74.0 - - - +
80A GLY* 1.3 59.8 + - - +
82A GLU* 3.5 14.1 + - + +
83A ASP* 2.9 53.6 + - - +
284A TYR* 3.6 25.8 - - + -
70B SER* 6.5 1.1 - - - -
96B ASN* 4.5 16.4 - - - +
98B ASP* 4.3 17.4 - - + +
103B LYS* 5.6 0.4 - - - -
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU 3.1 10.5 + - - -
77A ILE 3.5 4.3 - - - -
79A ARG* 1.3 76.5 - - - +
81A VAL* 1.3 50.8 + - - +
83A ASP* 4.0 0.7 - - - +
84A VAL* 2.7 37.1 + - - +
284A TYR* 3.4 38.1 - - - -
287A GLY 3.8 6.1 - - - -
288A GLU* 3.8 5.5 - - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 4.6 2.7 - - + -
64A LEU* 4.1 24.9 - - + -
77A ILE* 3.0 24.3 + - + +
78A ALA 3.6 7.0 - - - +
80A GLY* 1.3 73.8 - - - +
82A GLU* 1.3 60.4 + - - +
84A VAL* 3.2 5.0 - - - +
85A ALA* 2.9 31.9 + - - +
92A VAL* 4.3 18.8 - - + -
120A ILE* 3.9 31.9 - - + -
287A GLY* 3.4 24.9 - - - +
290A ALA* 4.8 2.5 - - + -
291A VAL* 4.2 7.1 - - + +
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Residues in contact with GLU 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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64A LEU* 5.6 0.2 - - + -
78A ALA 2.9 29.2 + - - +
79A ARG* 3.3 15.5 + - - +
81A VAL* 1.3 74.3 - - + +
83A ASP* 1.3 59.2 + - - +
85A ALA* 3.9 0.9 - - - +
86A LEU* 2.9 32.4 + - - +
92A VAL* 4.2 16.0 - - + +
94A ILE* 3.3 19.9 - - + +
69B MET* 4.1 3.5 - - - +
96B ASN* 3.3 34.7 + - - +
103B LYS* 3.4 24.4 + - - +
107B TYR* 2.6 28.7 + - - +
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Residues in contact with ASP 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 ARG* 2.9 34.6 + - - +
80A GLY 4.0 2.2 - - - +
82A GLU* 1.3 74.1 - - - +
84A VAL* 1.3 67.2 + - + +
86A LEU* 3.4 3.2 + - - +
87A ALA* 3.1 23.2 + - - +
284A TYR* 2.4 37.3 + - - +
288A GLU* 5.5 0.4 - - - +
98B ASP* 5.8 0.5 - - - +
103B LYS* 3.8 19.6 - - - +
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Residues in contact with VAL 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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80A GLY 2.7 25.4 - - - +
81A VAL 3.2 8.7 - - - +
83A ASP* 1.3 74.8 - - + +
85A ALA* 1.3 60.1 + - - +
87A ALA* 3.3 7.1 + - - +
88A HIS* 3.1 34.6 + - + +
288A GLU* 4.0 31.6 - - + +
291A VAL* 2.6 40.2 - - + -
292A SER* 4.7 6.1 - - - +
295A LEU* 6.0 0.9 - - - -
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Residues in contact with ALA 85 (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 ILE* 4.9 3.4 - - + -
81A VAL* 2.9 22.4 + - + +
82A GLU 3.9 0.9 - - - +
84A VAL* 1.3 73.1 - - - +
86A LEU* 1.3 62.6 + - - +
88A HIS* 3.1 9.0 + - - -
90A TYR* 2.8 46.0 + - + +
92A VAL* 3.8 25.8 - - + -
291A VAL* 4.4 14.9 - - + +
295A LEU* 5.3 1.1 - - - -
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Residues in contact with LEU 86 (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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82A GLU 2.9 21.5 + - - +
83A ASP* 4.1 3.1 - - - +
84A VAL 3.3 0.2 - - - -
85A ALA* 1.3 73.4 - - - +
87A ALA* 1.3 65.9 + - - +
89A GLY* 3.3 11.8 + - - -
90A TYR 3.8 11.0 - - - +
103B LYS* 5.5 13.2 - - + +
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Residues in contact with ALA 87 (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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83A ASP 3.1 14.5 + - - +
84A VAL* 3.4 12.3 - - - +
86A LEU* 1.3 78.1 - - - +
88A HIS* 1.3 70.6 + - + +
89A GLY 3.5 2.4 + - - -
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Residues in contact with HIS 88 (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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84A VAL* 3.1 23.8 + - + +
85A ALA 3.1 4.9 + - - +
87A ALA* 1.3 83.3 - - + +
89A GLY* 1.3 62.2 + - - +
90A TYR* 3.2 30.3 + + + -
295A LEU* 5.0 10.1 - - + -
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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