Contacts of the helix formed by residues 88 - 104 (chain A) in PDB entry 1IAP
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 GLY 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LEU* 1.3 74.5 - - - +
89A PRO* 1.3 67.5 - - - +
90A LYS* 3.1 4.3 + - - -
91A GLU* 3.2 16.8 + - - -
92A ALA* 2.7 32.9 + - - +
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Residues in contact with PRO 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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87A LEU 4.6 0.2 - - - +
88A GLY* 1.3 82.9 - - - +
90A LYS* 1.3 60.3 + - - +
92A ALA* 4.1 4.5 - - + +
93A LYS* 3.3 23.6 + - - +
132A GLU* 4.4 34.7 - - + +
135A GLN* 5.6 0.3 + - - -
136A ARG* 5.3 9.4 - - - +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLY 3.2 0.4 - - - -
89A PRO* 1.3 77.9 - - - +
91A GLU* 1.3 70.6 + - + +
93A LYS* 3.3 18.1 + - - +
94A LYS* 3.5 34.4 + - - +
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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 LEU* 4.1 28.4 - - + +
88A GLY* 3.2 21.2 + - - +
90A LYS* 1.3 79.9 - - + +
92A ALA* 1.3 58.8 + - - +
94A LYS* 3.2 11.4 + - - +
95A ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 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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84A LEU* 3.9 23.3 - - + +
87A LEU* 3.9 10.9 - - + +
88A GLY 2.7 24.6 + - - +
89A PRO* 4.2 4.7 - - + +
91A GLU* 1.3 72.8 - - - +
93A LYS* 1.3 56.6 + - - +
95A ALA* 3.8 7.7 - - - +
96A PHE* 2.9 23.2 + - - +
135A GLN* 3.2 24.2 + - - +
136A ARG* 6.1 3.1 - - - +
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Residues in contact with LYS 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 PRO 3.3 15.5 + - - +
90A LYS* 3.4 13.2 - - - +
91A GLU 3.1 0.6 - - - -
92A ALA* 1.3 78.8 - - - +
94A LYS* 1.3 63.0 + - + +
96A PHE* 3.4 6.1 + - - +
97A LEU* 3.3 49.4 + - + +
127A ALA* 2.8 31.6 + - - +
128A ASP* 5.0 3.1 - - - +
130A ILE* 3.5 34.1 - - - +
131A SER 6.1 0.2 - - - -
132A GLU* 5.9 6.7 - - + +
135A GLN* 3.4 16.4 + - - +
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Residues in contact with LYS 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 LYS* 3.5 34.6 + - - +
91A GLU* 3.2 10.2 + - - +
93A LYS* 1.3 76.2 - - + +
95A ALA* 1.3 64.3 + - - +
97A LEU* 3.3 24.0 + - + +
98A ASP* 3.3 19.6 + - - +
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Residues in contact with ALA 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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83A MET* 6.4 0.4 - - + -
84A LEU* 3.5 25.7 - - + +
87A LEU* 3.8 17.0 - - + -
91A GLU 2.9 18.0 + - - +
92A ALA* 3.8 3.8 - - - +
94A LYS* 1.3 78.1 - - - +
96A PHE* 1.3 56.5 + - - +
98A ASP* 3.4 11.1 + - - +
99A PHE* 2.9 27.7 + - - +
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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
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84A LEU* 3.9 8.7 - - + +
92A ALA 2.9 19.5 + - - +
93A LYS* 3.6 5.2 - - - +
94A LYS 3.2 0.2 - - - -
95A ALA* 1.3 75.2 - - - +
97A LEU* 1.3 68.0 + - + +
99A PHE* 3.2 18.3 + + - +
100A TYR* 2.7 39.5 + + + +
104A LEU* 4.7 8.5 - - + -
122A LEU* 4.4 16.2 - - + -
130A ILE* 4.6 18.6 - - + -
135A GLN* 3.6 35.0 - - + +
138A PHE* 4.2 28.3 - + + -
139A VAL* 3.8 26.2 - - + -
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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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93A LYS* 3.3 37.5 - - + +
94A LYS* 3.3 16.5 + - + +
96A PHE* 1.3 84.3 - - + +
98A ASP* 1.3 59.9 + - - +
100A TYR* 3.2 8.4 + - + +
101A HIS* 2.9 45.6 + - + +
127A ALA* 4.2 20.4 - - + -
130A ILE* 6.2 0.7 - - + -
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Residues in contact with ASP 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 LYS* 3.3 14.9 + - - +
95A ALA* 3.6 12.7 - - - +
96A PHE 3.2 0.2 - - - -
97A LEU* 1.3 74.9 - - - +
99A PHE* 1.3 60.9 + - - +
101A HIS* 3.2 9.8 + - - +
102A SER* 2.8 37.5 + - - +
224A LEU* 6.1 4.8 - - + +
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Residues in contact with PHE 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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77A CYS* 3.3 50.0 - - - -
80A HIS* 4.0 13.0 - - + -
81A ALA* 3.9 17.0 - - + -
84A LEU* 4.0 14.4 - - + -
95A ALA 2.9 15.4 + - - +
96A PHE* 3.3 27.6 - + - +
98A ASP* 1.3 76.0 - - - +
100A TYR* 1.3 59.2 + - - +
103A PHE* 3.0 51.6 + + - +
104A LEU* 3.7 29.3 + - + -
139A VAL* 4.7 9.6 - - + -
142A VAL* 4.1 11.0 - - + -
143A VAL* 5.3 0.2 - - + -
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PHE* 2.7 22.1 + + + +
97A LEU* 3.3 13.5 - - + +
98A ASP 3.2 0.2 - - - -
99A PHE* 1.3 76.3 - - - +
101A HIS* 1.3 79.1 + + - +
104A LEU* 2.9 45.7 + - + -
105A GLU* 3.0 53.7 + - + +
122A LEU* 3.8 43.9 + - + +
123A ASP* 4.4 11.5 + - - -
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Residues in contact with HIS 101 (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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97A LEU* 2.9 40.1 + - + +
98A ASP* 3.8 9.0 - - - +
100A TYR* 1.3 92.4 - + - +
102A SER* 1.3 58.5 + - - +
105A GLU* 3.1 36.4 + - - +
108A ALA* 3.3 20.6 - - - +
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Residues in contact with SER 102 (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 HIS* 5.7 2.7 + - - -
98A ASP* 2.8 20.8 + - - +
99A PHE* 4.6 0.2 - - - -
101A HIS* 1.3 79.2 - - - +
103A PHE* 1.3 82.8 + - - +
108A ALA* 3.3 13.7 - - - +
109A VAL 4.7 0.2 + - - -
110A LEU* 3.5 26.1 + - - +
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Residues in contact with PHE 103 (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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73A GLY 3.9 3.6 - - - -
76A LEU* 3.8 26.2 - - + -
77A CYS* 3.7 36.8 - - + -
80A HIS* 3.5 41.7 - + + -
99A PHE* 3.0 34.2 + + + +
102A SER* 1.3 91.7 - - - +
104A LEU* 1.3 64.7 + - + +
105A GLU 3.9 0.4 - - - -
108A ALA* 4.5 0.4 - - - -
110A LEU* 3.5 38.4 - - + +
111A ARG* 3.3 7.6 - - - +
112A VAL* 2.9 35.2 + - + +
221A ALA* 4.9 0.4 - - + -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PHE* 4.7 9.0 - - + -
99A PHE* 3.7 29.8 - - + +
100A TYR* 2.9 31.5 + - + +
103A PHE* 1.3 87.3 - - + +
105A GLU* 1.3 66.6 + - - +
111A ARG* 3.3 20.9 + - - -
112A VAL* 4.1 3.8 - - + -
114A VAL* 3.9 21.7 - - + +
118A VAL* 5.2 0.7 - - + -
122A LEU* 4.0 22.8 - - + +
138A PHE* 5.9 0.9 - - + -
142A VAL* 3.7 40.8 - - + -
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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