Contacts of the helix formed by residues 84 - 97 (chain A) in PDB entry 1J7H
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 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.2 47.6 - - + +
81A ASP* 2.7 31.1 + - + +
83A ASN* 1.3 78.0 - - - +
85A PHE* 1.3 61.3 + - - +
86A ALA 2.9 7.2 + - - -
87A ALA* 2.9 19.9 + - - +
88A VAL* 3.3 12.9 + - + +
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Residues in contact with PHE 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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77A VAL* 5.2 3.1 - - + -
79A VAL* 3.6 28.2 - - + +
81A ASP 3.5 3.2 + - - +
82A LEU* 3.3 29.3 + - + +
83A ASN 3.3 0.6 - - - -
84A ASP* 1.3 78.5 - - - +
86A ALA* 1.3 55.6 + - - +
87A ALA 3.1 0.4 - - - -
88A VAL* 3.6 18.2 - - + -
89A ASN* 2.6 67.1 + - + +
107A ARG* 3.1 32.5 - - - -
109A CYS* 3.9 26.5 - - + -
116B PRO* 6.3 3.6 - - + -
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Residues in contact with ALA 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 LEU 4.4 1.2 + - - +
83A ASN 3.8 15.3 + - - +
84A ASP 2.9 0.6 + - - -
85A PHE* 1.3 80.2 - - - +
87A ALA* 1.3 56.4 + - - +
89A ASN* 4.6 2.3 - - - +
90A ALA* 3.3 23.7 + - - +
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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
----------------------------------------------------------
47A ILE* 5.3 3.6 - - + -
48A VAL* 4.4 25.1 - - + +
84A ASP* 2.9 12.4 + - - +
86A ALA* 1.3 78.1 - - - +
88A VAL* 1.3 66.8 + - + +
89A ASN 3.4 0.2 - - - -
90A ALA* 3.9 3.9 - - - +
91A GLU* 3.1 24.8 + - - +
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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
----------------------------------------------------------
47A ILE* 3.8 24.0 - - + -
48A VAL* 5.9 0.7 - - - +
51A ALA* 4.0 27.1 - - + +
55A LEU* 6.2 2.7 - - + -
77A VAL* 5.9 7.0 - - + -
79A VAL* 5.8 4.7 - - + -
84A ASP* 3.5 17.7 - - + +
85A PHE* 3.2 22.2 + - + +
87A ALA* 1.3 76.4 - - - +
89A ASN* 1.3 54.9 + - - +
91A GLU* 3.6 3.3 - - - +
92A TYR* 2.6 48.1 + - + +
107A ARG* 5.6 0.7 - - - +
121A LEU* 5.7 4.5 - - + -
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Residues in contact with ASN 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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85A PHE* 2.6 55.2 + - + +
86A ALA* 4.6 3.6 - - - +
88A VAL* 1.3 72.0 - - - +
90A ALA* 1.3 65.1 + - - +
92A TYR* 4.0 5.6 - - - -
93A GLU* 3.1 24.3 + - - +
107A ARG* 3.8 6.9 + - - +
16B GLY* 5.3 1.6 - - - -
17B PRO* 3.9 23.9 - - - +
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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 ALA 3.3 20.3 + - - +
87A ALA* 3.9 5.8 - - - +
88A VAL 3.3 0.4 - - - -
89A ASN* 1.3 82.2 - - - +
91A GLU* 1.3 56.8 + - - +
93A GLU* 4.7 2.2 - - - +
94A ARG* 3.1 26.7 + - - +
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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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48A VAL* 5.0 17.7 - - + +
51A ALA* 5.4 2.8 - - + +
52A ARG* 3.7 32.0 + - - +
55A LEU* 4.6 10.6 - - - +
87A ALA 3.1 18.0 + - - +
88A VAL* 4.1 2.9 - - - +
90A ALA* 1.3 75.9 - - - +
92A TYR* 1.3 64.8 + - - +
93A GLU 3.4 0.7 - - - -
94A ARG* 3.9 6.6 - - + +
95A PHE* 3.1 31.8 + - - +
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Residues in contact with TYR 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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55A LEU* 3.8 25.6 - - + -
75A THR* 3.1 33.0 + - + +
77A VAL* 5.2 4.0 - - + -
88A VAL* 2.6 31.9 + - + +
89A ASN* 3.8 5.2 - - - +
91A GLU* 1.3 75.2 - - - +
93A GLU* 1.3 58.8 + - - +
95A PHE* 2.9 34.6 - + - -
96A PHE* 3.1 46.9 - + - -
105A PRO* 5.1 1.4 + - - +
107A ARG* 3.1 42.8 - - - +
123A ILE* 6.2 0.9 - - + -
17B PRO* 3.3 36.3 + - + -
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Residues in contact with GLU 93 (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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89A ASN* 3.1 17.3 + - - +
90A ALA 4.7 2.1 - - - +
92A TYR* 1.3 74.2 - - - +
94A ARG* 1.3 74.7 + - - +
95A PHE 3.2 2.5 + - - -
96A PHE* 3.5 4.4 + - - +
97A LYS* 3.5 25.1 + - - +
104A PHE* 3.6 19.5 - - + -
15B ILE 5.8 0.4 - - - -
16B GLY* 3.4 10.5 - - - +
17B PRO* 3.4 43.1 - - + -
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Residues in contact with ARG 94 (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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90A ALA 3.1 21.2 + - - +
91A GLU* 4.0 8.7 - - + +
92A TYR 3.4 0.2 - - - -
93A GLU* 1.3 87.3 + - - +
95A PHE* 1.3 58.1 + - - +
97A LYS* 4.5 2.7 - - - +
98A GLU* 2.8 53.3 + - - +
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Residues in contact with PHE 95 (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 ARG* 5.4 11.2 - - - +
55A LEU* 3.2 50.3 - - + -
59A LYS* 5.8 4.7 - - + -
69A ALA* 4.5 6.5 - - + -
72A ILE* 6.0 0.2 - - + -
91A GLU* 3.1 24.0 + - - +
92A TYR* 2.9 21.3 - + - -
93A GLU 3.2 0.2 - - - -
94A ARG* 1.3 78.9 - - - +
96A PHE* 1.3 91.5 + + - +
97A LYS 3.4 0.2 - - - -
98A GLU* 3.1 6.6 + - - -
99A ASN* 2.6 56.0 + - - +
101A HIS* 3.8 20.0 - + - -
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.7 0.7 - - + -
69A ALA 4.1 7.0 - - - -
72A ILE* 4.1 15.9 - - + -
92A TYR* 3.1 45.7 + + - +
93A GLU* 3.9 10.1 - - - +
95A PHE* 1.3 125.9 - + - +
97A LYS* 1.3 55.0 + - - +
99A ASN 2.8 3.1 + - - -
100A ASN 2.8 10.9 + - - -
101A HIS* 2.5 70.5 + - + +
104A PHE* 5.1 6.3 - + + -
105A PRO* 3.3 35.7 - - + -
17B PRO* 5.1 3.6 - - + -
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Residues in contact with LYS 97 (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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93A GLU* 3.5 22.4 + - - +
94A ARG* 5.0 2.2 - - - +
95A PHE 3.4 0.2 - - - -
96A PHE* 1.3 78.6 - - - +
98A GLU* 1.3 61.2 + - + +
99A ASN 3.1 1.1 + - - -
100A ASN* 3.3 10.0 + - - +
101A HIS 4.1 7.8 + - - +
102A PRO* 4.1 26.5 - - + -
104A PHE* 5.6 4.2 - - + -
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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