Contacts of the helix formed by residues 88 - 101 (chain A) in PDB entry 5I2S
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 SER 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A PHE* 5.3 0.2 - - - -
87A PRO* 1.3 79.3 - - - +
89A VAL* 1.3 64.3 + - - +
90A GLU* 3.1 9.7 + - - +
91A GLN* 2.9 37.1 + - - +
92A CYS* 3.4 21.7 + - - -
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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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88A SER* 1.3 74.4 - - - +
90A GLU* 1.3 71.4 + - + +
91A GLN 3.2 0.2 - - - -
92A CYS* 3.1 8.1 + - - +
93A LYS* 3.0 28.6 + - + +
156A TYR* 4.3 9.2 - - - +
157A ILE* 3.4 33.4 - - + -
168A HIS* 3.7 8.3 - - + +
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Residues in contact with GLU 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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88A SER* 3.1 7.5 + - - +
89A VAL* 1.3 84.6 - - + +
91A GLN* 1.3 56.8 + - - +
93A LYS* 3.4 9.1 + - + +
94A GLU* 2.9 29.9 + - - +
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Residues in contact with GLN 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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85A PHE* 4.2 19.8 - - - -
87A PRO* 3.4 16.2 - - + +
88A SER* 2.9 44.4 + - - +
90A GLU* 1.3 75.2 - - + +
92A CYS* 1.3 59.7 + - - +
94A GLU* 3.2 15.1 + - - +
95A SER* 2.9 31.7 + - - -
125A VAL* 4.7 13.3 - - - +
127A VAL* 4.2 18.4 - - + +
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Residues in contact with CYS 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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59A CYS* 2.0 52.2 - - + -
87A PRO* 3.8 9.6 - - - -
88A SER 3.4 15.2 + - - -
89A VAL* 3.1 6.8 + - - +
91A GLN* 1.3 78.5 - - - +
93A LYS* 1.3 57.7 + - - +
95A SER* 3.1 4.9 + - - -
96A ILE* 2.9 34.8 + - + +
129A VAL* 4.0 0.4 - - + +
166A THR* 4.1 6.3 - - - -
168A HIS* 3.3 30.1 - - + +
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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 VAL* 3.0 21.6 + - + +
90A GLU* 3.8 10.1 - - + +
92A CYS* 1.3 75.0 - - - +
94A GLU* 1.3 57.0 + - - +
96A ILE* 3.8 12.7 - - + +
97A GLU* 2.9 30.1 + - - +
156A TYR* 4.1 30.4 + - - -
157A ILE* 4.7 0.7 - - - -
168A HIS* 3.3 31.5 + - + +
169A SER 3.8 19.6 + - - -
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Residues in contact with GLU 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 GLU* 2.9 15.4 + - - +
91A GLN* 3.4 19.1 - - - +
92A CYS 3.1 0.2 - - - -
93A LYS* 1.3 76.8 - - - +
95A SER* 1.3 57.9 + - - +
97A GLU* 3.2 7.9 + - + +
98A GLN* 3.0 56.3 + - + +
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Residues in contact with SER 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 GLN 2.9 9.4 + - - -
92A CYS 3.6 6.5 - - - -
94A GLU* 1.3 72.9 - - - +
96A ILE* 1.3 59.5 + - - +
98A GLN* 3.6 10.0 + - - -
99A THR* 2.3 39.9 + - - -
104A TRP* 3.8 6.7 + - - -
127A VAL* 2.5 47.3 + - - +
129A VAL* 3.6 16.6 - - - -
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Residues in contact with ILE 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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57A TRP* 3.4 55.2 - - + +
59A CYS* 5.7 0.2 - - + -
92A CYS 2.9 22.3 + - - +
93A LYS* 3.9 16.2 - - + +
95A SER* 1.3 75.0 - - - +
97A GLU* 1.3 64.0 + - - +
99A THR* 3.3 1.9 + - - -
100A LYS* 2.9 36.4 + - + +
129A VAL* 3.6 22.0 - - + -
168A HIS* 3.7 27.4 - - + +
169A SER 5.9 0.2 - - - +
170A ASP* 5.0 1.8 - - - +
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Residues in contact with GLU 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 2.9 19.4 + - - +
94A GLU* 3.2 9.6 + - + +
96A ILE* 1.3 74.7 - - - +
98A GLN* 1.3 66.4 + - + +
100A LYS* 3.0 10.4 + - - +
101A GLN* 2.7 59.4 + - - +
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Residues in contact with GLN 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 GLU* 3.0 41.7 + - + +
95A SER* 3.9 4.3 + - - -
97A GLU* 1.3 77.3 - - + +
99A THR* 1.3 60.8 + - - +
101A GLN* 4.4 4.5 - - - +
102A GLY 3.1 2.8 + - - -
103A THR* 2.8 55.8 + - - +
104A TRP* 3.3 27.8 + - + -
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Residues in contact with THR 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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57A TRP* 4.2 21.5 - - + -
95A SER 2.3 27.5 + - - -
96A ILE* 3.8 4.0 - - - -
98A GLN* 1.3 78.3 - - - +
100A LYS* 1.3 63.5 + - - +
102A GLY* 3.2 12.4 + - - -
104A TRP* 3.6 22.9 - - + +
129A VAL* 3.2 23.5 - - - +
131A PRO* 6.1 0.9 - - + -
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Residues in contact with LYS 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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57A TRP* 3.7 20.2 - - + -
96A ILE* 2.9 35.8 + - + +
97A GLU* 3.7 9.2 - - - +
99A THR* 1.3 78.6 - - - +
101A GLN* 1.3 62.9 + - + +
102A GLY 3.4 0.7 + - - -
170A ASP* 2.9 36.1 + - - +
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Residues in contact with GLN 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 GLU* 2.7 49.1 + - - +
98A GLN* 4.4 2.6 - - - +
100A LYS* 1.3 77.1 - - + +
102A GLY* 1.3 59.4 + - - +
103A THR* 3.3 26.1 + - + +
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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