Contacts of the helix formed by residues 81 - 100 (chain A) in PDB entry 2IAI
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 THR 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLY* 1.3 76.6 - - - -
82A ALA* 1.3 64.2 + - - +
83A ALA* 3.6 6.3 + - - +
84A GLU* 2.9 42.0 + - - +
85A ARG* 2.9 22.2 + - - +
141A GLU* 3.8 11.9 - - - +
143A ASP* 4.3 11.2 + - - +
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Residues in contact with ALA 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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80A GLY 3.9 0.4 + - - -
81A THR* 1.3 70.8 - - - +
83A ALA* 1.3 58.0 + - - +
85A ARG* 3.3 13.8 + - - +
86A LEU* 2.8 29.5 + - - +
134A LEU* 4.1 8.5 - - + +
137A ASP* 3.6 12.8 - - + +
138A ALA* 3.3 29.8 - - - +
141A GLU* 2.9 30.0 + - - +
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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
----------------------------------------------------------
81A THR* 3.1 4.0 + - - +
82A ALA* 1.3 78.0 - - - +
84A GLU* 1.3 60.3 + - + +
86A LEU* 3.8 4.6 - - - +
87A GLU* 3.0 30.5 + - - +
138A ALA* 3.9 12.8 - - + +
141A GLU* 4.5 1.0 + - - -
143A ASP* 3.6 35.6 + - + +
144A VAL* 5.0 5.2 - - + -
202A PHE* 4.3 9.4 - - + -
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Residues in contact with GLU 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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76A HIS 4.2 1.7 - - - +
79A VAL 4.9 1.8 - - - +
80A GLY* 3.3 13.0 - - - -
81A THR* 2.9 47.4 + - - +
83A ALA* 1.3 75.4 - - + +
85A ARG* 1.3 63.6 + - - +
87A GLU* 3.4 6.4 + - - +
88A TYR* 3.0 23.9 + - - +
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS 3.5 9.6 - - - +
77A ALA 3.4 28.0 - - - +
78A ARG* 3.2 27.4 + - - +
79A VAL* 3.2 24.6 + - - +
80A GLY 2.9 27.4 + - - +
81A THR 2.9 12.3 + - - +
82A ALA* 3.6 11.2 - - - +
84A GLU* 1.3 75.8 - - - +
86A LEU* 1.3 58.5 + - - +
88A TYR* 3.3 3.3 + - - +
89A VAL* 2.9 34.6 + - - +
134A LEU* 4.6 16.9 - - + +
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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 ALA 2.8 17.6 + - - +
83A ALA* 3.8 5.4 - - - +
84A GLU 3.3 0.2 - - - -
85A ARG* 1.3 78.3 - - - +
87A GLU* 1.3 58.5 + - - +
89A VAL* 3.2 6.4 + - + +
90A VAL* 2.9 41.9 + - + +
131A VAL* 3.9 30.5 - - + +
134A LEU* 4.2 21.7 - - + +
135A LEU* 4.0 37.5 - - + +
138A ALA* 4.7 1.8 - - + -
144A VAL* 4.5 11.4 - - + -
201A VAL* 6.3 0.9 - - + -
202A PHE* 4.0 22.7 - - + -
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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 ALA 3.0 17.8 + - - +
84A GLU* 3.9 5.3 - - - +
86A LEU* 1.3 76.2 - - - +
88A TYR* 1.3 63.8 + - - +
90A VAL* 3.3 2.1 + - - +
91A ARG* 3.0 61.3 + - - +
198A ALA* 4.0 6.0 - - + +
202A PHE* 3.5 40.1 - - + +
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Residues in contact with TYR 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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71A ILE* 4.4 2.5 - - + -
74A GLU* 2.6 42.3 + - + +
76A HIS* 3.5 34.8 + + + +
77A ALA* 3.4 30.3 - - + -
84A GLU 3.0 18.3 + - - +
85A ARG 3.5 3.8 - - - +
87A GLU* 1.3 78.0 - - - +
89A VAL* 1.3 60.1 + - + +
91A ARG* 3.3 11.1 + - + +
92A ARG* 2.9 56.4 + - + +
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Residues in contact with VAL 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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71A ILE* 4.0 12.5 - - + +
72A LEU* 4.0 23.6 - - + -
77A ALA* 3.7 26.2 - - + -
85A ARG 2.9 21.0 + - - +
86A LEU* 3.2 7.4 + - + +
88A TYR* 1.3 75.7 - - - +
90A VAL* 1.3 57.7 + - + +
92A ARG* 3.3 2.1 + - - +
93A MSE 2.8 54.0 + - + +
127A PHE* 5.0 0.2 - - + -
131A VAL* 4.2 16.6 - - + -
134A LEU* 3.8 17.3 - - + -
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Residues in contact with VAL 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 LEU* 2.9 33.0 + - + +
87A GLU 3.7 4.7 - - - +
89A VAL* 1.3 77.5 - - + +
91A ARG* 1.3 64.0 + - - +
93A MSE 3.2 10.1 + - - +
94A VAL* 3.1 22.5 + - - +
131A VAL* 5.9 2.2 - - + -
157A VAL* 4.4 19.1 - - + -
158A PHE* 6.4 0.7 - - + -
161A ILE* 4.1 11.1 - - + +
197A VAL* 3.9 25.8 - - + -
198A ALA* 4.7 7.2 - - + +
201A VAL* 4.3 14.1 - - + -
202A PHE* 4.4 15.9 - - + -
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Residues in contact with ARG 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 49.8 + - - +
88A TYR* 3.7 9.9 - - + +
90A VAL* 1.3 75.0 - - - +
92A ARG* 1.3 64.9 + - + +
94A VAL* 3.1 9.1 + - - +
95A GLU* 3.1 28.8 + - - +
194A VAL* 3.7 25.8 - - + +
195A ASP* 2.9 32.1 + - - +
198A ALA* 3.4 27.7 - - + +
199A ARG* 5.4 5.7 - - - +
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Residues in contact with ARG 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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67A GLU* 5.2 5.9 + - - -
71A ILE* 3.6 24.3 - - + +
74A GLU* 2.9 33.9 + - - +
88A TYR* 2.9 53.7 + - + +
89A VAL 3.7 0.2 - - - +
91A ARG* 1.3 73.2 - - + +
93A MSE 1.3 61.0 + - - +
95A GLU* 2.9 52.4 + - - +
96A VAL* 2.8 50.7 + - - +
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Residues in contact with MSE 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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68A LEU* 4.5 11.8 - - + +
71A ILE* 3.8 17.5 - - + -
89A VAL* 2.8 32.8 + - + +
90A VAL* 3.2 9.2 + - - +
92A ARG* 1.3 75.8 - - - +
94A VAL* 1.3 63.3 + - - +
96A VAL* 3.9 2.0 - - - +
97A LEU* 3.0 26.3 + - - +
127A PHE* 4.0 28.0 - - + -
131A VAL* 4.6 0.9 - - - -
158A PHE* 3.8 41.3 - - + -
161A ILE* 4.1 31.9 - - + +
162A ASN* 4.8 7.0 - - - +
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Residues in contact with VAL 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 VAL 3.1 14.3 + - - +
91A ARG* 3.1 9.1 + - - +
93A MSE 1.3 76.2 - - - +
95A GLU* 1.3 62.8 + - - +
97A LEU* 3.3 4.7 + - - +
98A MSE 3.1 33.1 + - + +
161A ILE* 4.2 16.6 - - + -
164A ILE* 4.2 8.3 - - + -
193A VAL* 3.9 22.2 - - + -
194A VAL* 3.6 24.9 - - + -
197A VAL* 3.7 33.7 - - + -
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Residues in contact with GLU 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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91A ARG* 3.1 17.0 + - - +
92A ARG* 2.9 42.6 + - - +
94A VAL* 1.3 76.2 - - - +
96A VAL* 1.3 58.7 + - - +
98A MSE 3.4 12.4 + - + +
99A ALA* 3.0 29.2 + - - +
194A VAL* 3.7 23.3 - - + +
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Residues in contact with VAL 96 (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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67A GLU* 3.8 38.6 - - + +
68A LEU* 4.1 20.9 - - + -
71A ILE* 3.9 18.2 - - + -
92A ARG* 2.8 41.1 + - - +
93A MSE 3.9 2.9 - - - +
95A GLU* 1.3 70.0 - - - +
97A LEU* 1.3 62.5 + - - +
99A ALA* 4.5 4.3 - - - -
100A GLU* 2.8 36.8 + - + +
104A VAL* 4.5 7.4 - - + -
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Residues in contact with LEU 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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68A LEU* 5.7 1.1 - - + +
93A MSE 3.0 17.5 + - - +
94A VAL* 3.3 4.7 + - - +
96A VAL* 1.3 76.2 - - - +
98A MSE 1.3 63.1 + - + +
101A LEU* 3.1 30.4 - - + +
104A VAL* 4.3 20.2 - - + -
161A ILE* 3.1 34.8 - - + +
162A ASN* 3.8 14.8 - - - +
164A ILE* 3.6 30.3 - - + -
165A VAL* 3.6 33.9 - - + +
168A TYR* 5.4 0.4 - - + -
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Residues in contact with MSE 98 (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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94A VAL* 3.1 22.9 + - + +
95A GLU* 3.8 10.3 - - + +
97A LEU* 1.3 84.5 - - + +
99A ALA* 1.3 64.2 + - - +
100A GLU 3.5 0.2 + - - -
101A LEU* 3.6 12.0 + - - +
164A ILE* 4.6 3.8 - - + -
168A TYR* 3.5 61.4 + - + +
170A PRO* 6.0 0.7 - - - +
190A GLU* 3.7 31.9 - - + +
193A VAL* 4.1 15.7 - - - -
194A VAL* 3.7 28.5 - - + -
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Residues in contact with ALA 99 (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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95A GLU 3.0 18.5 + - - +
96A VAL* 3.9 3.8 - - - +
98A MSE 1.3 78.8 - - - +
100A GLU* 1.3 74.0 - - + +
101A LEU 3.5 1.1 + - - -
102A PRO* 5.1 1.9 - - - +
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Residues in contact with GLU 100 (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 ARG* 2.8 47.2 + - - +
64A ALA* 5.3 1.8 - - - -
67A GLU* 4.0 30.2 - - + +
96A VAL* 2.8 21.2 + - + +
97A LEU 3.9 2.2 - - - -
99A ALA* 1.3 90.0 - - + +
101A LEU* 1.3 63.1 + - - +
102A PRO* 3.3 5.6 - - - -
103A TYR* 3.0 19.9 + - + -
104A VAL* 2.9 29.7 + - + -
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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