Contacts of the helix formed by residues 85 - 99 (chain A) in PDB entry 1I4A
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 PRO 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR* 4.4 4.0 - - + -
49A GLN* 3.4 28.7 - - + +
52A ARG* 3.7 16.8 - - - +
83A MET 3.8 0.2 - - - -
84A THR* 1.3 94.1 - - + +
86A THR* 1.3 61.0 + - - +
87A VAL* 3.4 1.6 - - + +
88A LEU* 3.2 22.4 + - + +
89A TYR* 2.9 26.9 + - - +
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Residues in contact with THR 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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45A THR* 4.2 17.7 + - - +
84A THR 3.5 2.9 + - - -
85A PRO* 1.3 70.5 - - - +
87A VAL* 1.3 68.2 + - + +
89A TYR* 3.4 6.2 + - - +
90A ASP* 3.3 29.8 + - - +
273A SER 6.1 0.9 - - - +
277A ILE* 6.1 5.6 - - + -
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Residues in contact with VAL 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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85A PRO* 3.4 1.7 - - + +
86A THR* 1.3 81.3 - - + +
88A LEU* 1.3 63.2 + - - +
90A ASP* 3.2 9.5 + - - +
91A VAL* 3.0 20.3 + - - +
119A GLU 6.0 0.2 - - - +
122A ARG* 4.4 23.8 - - + +
123A ILE* 4.3 22.7 - - + +
126A THR* 3.8 28.7 - - + +
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Residues in contact with LEU 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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52A ARG* 6.0 0.9 - - - +
84A THR* 4.0 12.1 - - + -
85A PRO* 3.2 25.7 + - + +
87A VAL* 1.3 80.1 - - - +
89A TYR* 1.3 58.0 + - - +
91A VAL* 3.2 8.0 + - + -
92A GLN* 2.8 65.3 + - + +
126A THR* 4.7 6.0 - - + +
130A GLN* 3.8 37.5 - - + +
131A TYR* 5.6 0.2 - - - +
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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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77A GLN* 5.3 1.3 + - - +
81A GLY* 3.7 25.9 - - - -
84A THR* 3.6 20.1 - - + +
85A PRO 2.9 16.9 + - - +
86A THR* 3.7 7.2 - - - +
88A LEU* 1.3 78.6 - - - +
90A ASP* 1.3 60.6 + - - +
92A GLN* 3.4 6.1 + - + -
93A GLU* 2.9 58.1 + - + +
268A ILE* 4.0 9.7 - - - +
269A ARG* 3.4 41.2 + - + +
272A VAL* 3.7 33.0 - - + +
273A SER* 4.4 12.1 - - - -
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Residues in contact with ASP 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 THR* 3.3 17.2 + - - +
87A VAL* 3.2 10.5 + - - +
89A TYR* 1.3 85.3 - - - +
91A VAL* 1.3 63.0 + - - +
93A GLU* 3.2 2.9 + - - +
94A LEU* 3.0 31.2 + - - +
111A ILE* 3.9 13.2 - - + +
115A ARG* 2.7 49.2 + - - +
123A ILE* 3.6 26.4 - - + +
269A ARG* 5.9 0.9 - - - -
273A SER* 4.9 0.3 - - - -
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Residues in contact with VAL 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 VAL 3.0 17.7 + - - +
88A LEU* 3.5 11.7 - - + +
90A ASP* 1.3 76.3 - - - +
92A GLN* 1.3 57.3 + - - +
94A LEU* 3.3 5.8 + - - +
95A ARG* 3.1 26.0 + - - +
123A ILE* 3.6 33.9 - - + +
126A THR* 3.6 28.7 - - + +
127A TYR* 3.8 18.8 - - + +
130A GLN* 4.5 6.1 - - + -
131A TYR* 3.5 25.6 - - + +
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Residues in contact with GLN 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 THR* 3.7 22.5 + - - +
88A LEU* 2.8 50.4 + - + +
89A TYR* 4.0 7.7 - - + +
91A VAL* 1.3 72.9 - - - +
93A GLU* 1.3 60.2 + - - +
95A ARG* 3.8 0.9 - - - +
96A LYS* 3.1 28.1 + - - +
130A GLN* 5.5 3.6 - - - +
131A TYR* 3.6 19.0 + - - +
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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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77A GLN* 4.9 1.6 - - - +
89A TYR* 2.9 50.0 + - + +
90A ASP* 3.2 4.9 + - - +
92A GLN* 1.3 77.4 - - - +
94A LEU* 1.3 60.1 + - - +
96A LYS* 3.2 36.8 + - - +
97A ALA* 3.0 27.7 + - - +
107A CYS* 3.6 6.6 - - - -
111A ILE* 3.9 15.5 - - + -
265A ASP 4.7 0.9 - - - +
269A ARG* 2.9 46.1 + - + +
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Residues in contact with LEU 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 ASP 3.0 18.8 + - - +
91A VAL* 3.7 4.7 - - - +
93A GLU* 1.3 73.8 - - - +
95A ARG* 1.3 66.1 + - - +
97A ALA* 3.2 14.1 + - - +
98A MET* 3.2 22.6 + - + +
107A CYS* 4.5 0.7 - - - +
108A LEU* 3.9 30.0 - - + +
111A ILE* 3.7 38.6 - - + -
112A LEU* 4.7 9.9 - - + -
123A ILE* 3.6 31.0 - - + -
127A TYR* 4.5 2.2 - - + -
135A LEU* 4.2 28.7 - - + -
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Residues in contact with ARG 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 VAL 3.1 10.1 + - - +
92A GLN 3.8 2.9 - - - +
94A LEU* 1.3 77.9 - - - +
96A LYS* 1.3 64.2 + - - +
98A MET* 2.9 17.3 + - - +
99A LYS* 3.0 57.5 + - + +
127A TYR* 3.2 26.6 - - + -
131A TYR* 3.5 51.4 - - + +
133A ARG* 3.1 29.1 - - - +
138A ASP* 4.4 1.9 + - - -
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Residues in contact with LYS 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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77A GLN* 3.4 25.1 + - - +
92A GLN 3.1 17.8 + - - +
93A GLU* 3.2 38.0 + - - +
95A ARG* 1.3 76.4 - - - +
97A ALA* 1.3 62.3 + - - +
98A MET 3.2 0.7 + - - -
99A LYS* 3.5 19.8 + - - +
265A ASP* 3.6 20.1 + - - +
269A ARG* 5.6 0.2 - - - +
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Residues in contact with ALA 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 3.0 16.0 + - - +
94A LEU 3.4 10.3 - - - +
96A LYS* 1.3 78.3 - - - +
98A MET* 1.3 59.5 + - - +
102A GLY 3.8 2.9 - - - +
103A THR* 3.3 8.5 - - - +
104A ASP* 2.9 57.0 + - + +
107A CYS* 3.9 10.1 - - - -
108A LEU* 3.8 13.9 - - + -
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Residues in contact with MET 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 LEU 3.2 18.1 + - - +
95A ARG* 2.9 14.7 + - - +
97A ALA* 1.3 81.8 - - - +
99A LYS* 1.3 62.3 + - - +
100A GLY 3.9 5.5 + - - +
102A GLY 4.6 3.1 - - - +
103A THR* 4.5 3.7 + - + -
108A LEU* 4.1 24.5 - - + -
127A TYR* 3.5 20.6 - - - +
135A LEU* 3.8 25.4 - - + -
138A ASP* 3.7 35.7 - - + +
139A ILE* 3.8 12.1 - - + -
142A ASP* 2.8 35.0 - - + +
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Residues in contact with LYS 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 ARG* 3.0 47.2 + - + +
96A LYS* 3.5 14.2 + - - +
98A MET* 1.3 80.2 + - - +
100A GLY* 1.3 83.5 + - - +
102A GLY 3.7 8.8 - - - +
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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