Contacts of the helix formed by residues 78 - 92 (chain A) in PDB entry 3IP7
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.8 6.1 - - - +
15A ASN* 3.9 0.3 + - - -
51A ASP* 4.4 1.4 + - - -
53A SER* 2.8 43.4 + - - +
76A HIS* 4.6 1.2 - - - +
77A PHE* 1.3 84.9 - - - +
79A SER* 1.3 61.1 + - - +
80A GLY 4.2 2.2 - - - +
81A VAL* 3.2 19.7 + - + +
82A SER* 2.9 29.8 + - - -
101A ALA* 4.2 0.2 - - - -
202A LEU* 3.7 19.6 - - - +
357A CA 4.2 5.6 - - - -
500A VAL* 3.2 18.3 - - - +
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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
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77A PHE 3.7 0.2 + - - -
78A ASN* 1.3 72.5 - - - +
80A GLY* 1.3 57.2 + - - +
82A SER* 4.4 0.7 - - - -
83A ILE* 3.0 43.1 + - - +
101A ALA* 3.7 9.8 - - - +
102A THR 3.3 3.1 + - - -
103A ASN* 2.9 41.3 + - - +
106A PHE* 5.7 0.8 - - - +
149A PRO* 4.8 0.9 - - - -
150A TYR* 4.0 7.8 - - - +
357A CA 3.7 4.7 - - - -
500A VAL* 2.5 33.1 + - - -
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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
----------------------------------------------------------
55A PRO* 3.5 19.1 - - - +
78A ASN* 3.2 0.8 - - - +
79A SER* 1.3 76.2 - - - +
81A VAL* 1.3 59.3 + - - +
83A ILE* 5.2 1.3 - - - -
84A PRO* 3.1 23.2 - - - +
149A PRO* 3.9 23.1 - - - +
357A CA 2.9 18.1 - - - -
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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
----------------------------------------------------------
51A ASP* 3.6 14.1 - - + +
53A SER* 3.8 20.4 - - - +
54A ASP 3.8 27.1 - - - +
55A PRO* 3.8 6.1 - - + +
58A GLY* 4.2 10.4 - - - -
76A HIS* 3.4 34.8 - - + +
78A ASN* 3.2 21.4 + - + +
79A SER 3.1 0.2 - - - -
80A GLY* 1.3 79.3 - - - +
82A SER* 1.3 65.1 + - - +
83A ILE 3.4 0.2 - - - -
84A PRO* 3.3 5.8 - - - +
85A ALA* 3.1 21.9 + - + +
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS* 3.0 34.4 + - - +
78A ASN 2.9 18.8 + - - -
79A SER 3.9 1.8 - - - -
81A VAL* 1.3 75.4 - - - +
83A ILE* 1.3 60.1 + - - +
85A ALA* 4.6 2.2 - - - -
86A SER* 2.8 35.0 + - - -
96A GLU* 3.7 14.1 - - - +
98A THR* 4.2 0.2 + - - -
101A ALA* 3.6 15.0 - - - +
106A PHE* 3.6 14.8 - - - -
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Residues in contact with ILE 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 SER* 3.0 26.2 + - - +
80A GLY* 5.2 0.9 - - - -
82A SER* 1.3 74.0 - - - +
84A PRO* 1.4 69.4 - - + +
86A SER* 2.5 24.1 + - - -
87A GLU* 3.7 6.3 + - - +
103A ASN* 3.9 15.7 - - + +
105A VAL* 3.9 31.2 - - + -
106A PHE* 3.9 25.8 - - + +
109A ARG* 3.0 28.5 + - - +
149A PRO* 5.0 9.2 - - + -
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Residues in contact with PRO 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PRO* 4.6 11.2 - - + +
59A ILE* 4.1 25.6 - - + +
80A GLY* 3.1 28.9 - - - +
81A VAL* 3.3 12.8 - - - +
83A ILE* 1.4 92.7 - - + +
85A ALA* 1.3 62.8 + - - +
87A GLU* 3.1 31.9 + - - +
88A VAL* 3.5 8.7 + - - +
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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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58A GLY 4.4 9.2 - - - +
59A ILE* 4.8 3.7 - - - +
62A ALA* 4.1 15.0 - - + -
76A HIS* 3.9 17.0 - - + +
81A VAL* 3.1 20.5 + - + +
82A SER 4.0 2.5 - - - +
84A PRO* 1.3 77.0 - - - +
86A SER* 1.3 58.2 + - - +
88A VAL* 3.1 8.8 + - - +
89A TYR* 3.0 47.3 + - + -
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER 2.8 11.6 + - - -
83A ILE 2.5 22.2 + - - -
85A ALA* 1.3 74.5 - - - +
87A GLU* 1.3 54.1 + - - +
89A TYR* 3.8 3.6 - - - -
90A ALA* 2.7 36.3 + - - +
96A GLU* 3.1 22.4 + - - -
106A PHE* 3.8 11.0 - - - -
109A ARG* 2.8 22.0 + - - -
111A LEU* 3.8 1.5 - - - +
113A ASN* 3.3 4.0 + - - +
114A THR* 3.9 11.4 - - - -
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Residues in contact with GLU 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 ILE* 3.9 6.3 - - - +
84A PRO* 3.1 23.8 + - - +
86A SER* 1.3 74.3 + - - +
88A VAL* 1.3 69.2 - - + +
90A ALA* 3.2 7.5 + - - +
91A GLU* 3.0 28.0 + - - +
109A ARG* 3.9 20.6 + - - +
111A LEU* 4.7 6.1 - - + -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.5 20.6 - - + -
62A ALA* 3.8 21.5 - - + -
63A ASN* 3.5 26.0 - - - +
66A VAL* 4.0 16.1 - - + +
84A PRO 3.5 9.6 + - - +
85A ALA* 3.1 10.0 + - - +
87A GLU* 1.3 81.7 - - + +
89A TYR* 1.3 61.3 + - + +
91A GLU* 4.9 2.0 - - - -
92A ASN* 2.8 32.8 + - - +
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Residues in contact with TYR 89 (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 ALA* 3.3 38.6 - - + +
65A PHE* 3.3 21.3 - + + -
73A VAL* 3.8 21.6 - - + +
76A HIS* 2.8 30.9 + - - -
85A ALA* 3.0 19.8 + - + -
86A SER 3.7 0.7 - - - +
87A GLU 3.1 0.2 - - - -
88A VAL* 1.3 77.3 - - + +
90A ALA* 1.3 65.6 + - - +
92A ASN 3.0 12.1 + - - -
94A ILE* 3.1 58.6 + - + +
96A GLU* 3.2 38.4 - - + -
113A ASN* 3.4 7.9 - - - +
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Residues in contact with ALA 90 (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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86A SER 2.7 21.7 + - - +
87A GLU* 3.2 6.3 + - - +
89A TYR* 1.3 71.9 - - - +
91A GLU* 1.3 61.7 + - + +
92A ASN 3.6 0.2 + - - -
93A GLY 4.0 1.2 + - - -
111A LEU* 3.7 24.5 - - + -
112A TRP* 2.9 30.6 + - + +
113A ASN* 3.1 24.7 - - - +
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Residues in contact with GLU 91 (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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87A GLU 3.0 17.1 + - - +
88A VAL* 3.9 1.3 - - - +
90A ALA* 1.3 78.5 - - + +
92A ASN* 1.3 73.5 + - - +
93A GLY 3.5 1.6 + - - -
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Residues in contact with ASN 92 (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 ASN* 5.5 0.5 - - - +
66A VAL* 3.6 42.8 - - + +
88A VAL* 2.8 24.5 + - - +
89A TYR 3.0 3.7 + - - +
91A GLU* 1.3 90.6 + - - +
93A GLY* 1.3 61.6 + - - +
94A ILE* 3.3 12.5 - - - +
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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