Contacts of the strand formed by residues 116 - 128 (chain C) in PDB entry 5IPN
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 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C LEU 3.4 4.7 - - - +
104C ILE* 2.9 54.5 + - + +
115C LYS* 1.3 104.9 - - - +
117C ILE* 1.3 62.4 + - - +
118C LYS* 4.2 5.2 - - + -
484C LEU* 4.4 13.0 - - - +
485C ASP* 5.3 8.9 + - - +
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.5 36.6 - - + -
102C LEU 3.3 2.0 - - - -
103C VAL* 4.0 20.6 - - + -
113C THR* 3.7 22.4 - - + +
114C VAL* 5.0 8.1 - - + -
115C LYS 4.3 0.6 - - - +
116C ASP* 1.3 78.4 - - - +
118C LYS* 1.3 61.8 + - - +
119C GLU* 4.1 3.8 + - + +
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LEU 3.9 1.0 - - - +
101C ARG* 3.5 1.2 - - - -
102C LEU* 2.7 54.8 + - + +
116C ASP* 4.2 4.7 - - + -
117C ILE* 1.3 75.5 - - - +
119C GLU* 1.3 58.8 + - - +
120C GLN* 4.3 0.4 + - + -
484C LEU 5.2 3.1 - - - +
485C ASP* 2.7 35.1 + - - +
486C THR* 4.3 0.8 + - - +
487C LEU 4.1 12.7 + - - +
488C MET* 3.1 43.3 - - + -
489C PRO* 4.7 10.7 - - + +
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Residues in contact with GLU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C VAL* 3.7 10.7 - - + +
99C LYS* 3.5 25.5 + - - +
100C LEU 3.1 31.2 + - - +
101C ARG* 3.7 27.8 - - + +
117C ILE* 4.1 4.3 + - + +
118C LYS* 1.3 74.1 - - - +
120C GLN* 1.3 67.7 + - - +
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Residues in contact with GLN 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C VAL 3.7 1.0 - - - +
99C LYS* 4.3 2.9 - - - -
100C LEU* 2.9 34.0 + - - +
118C LYS 5.8 0.4 - - - -
119C GLU* 1.3 81.4 - - - +
121C GLU* 1.3 63.1 + - - +
122C VAL* 3.9 6.1 + - + +
488C MET* 3.7 22.1 - - - +
489C PRO* 3.6 27.4 - - + +
490C GLN* 3.1 43.8 - - - +
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Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C TYR 5.5 0.2 - - - -
74C ARG* 2.7 37.0 + - - +
97C ARG* 3.2 36.4 - - + +
98C VAL 3.4 12.8 - - - +
99C LYS* 4.1 28.9 - - + +
120C GLN* 1.3 77.0 - - - +
122C VAL* 1.3 64.1 + - - +
123C TYR 4.3 0.3 + - - -
490C GLN* 4.5 6.2 - - - +
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Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LEU 3.8 0.9 - - - +
97C ARG* 3.5 3.0 - - - -
98C VAL* 2.8 39.4 + - + +
100C LEU* 5.2 4.5 - - + -
120C GLN* 4.1 16.4 - - + +
121C GLU* 1.3 76.8 - - - +
123C TYR* 1.3 75.3 + - - +
124C MET* 3.8 4.4 + - + +
489C PRO* 4.8 3.6 - - + -
490C GLN* 3.4 44.0 - - + +
493C ILE* 4.2 33.7 - - + -
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Residues in contact with TYR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PRO* 4.0 11.2 - - + -
96C LEU 3.7 17.5 - - - -
97C ARG* 4.4 16.9 - - + +
121C GLU 4.3 0.6 + - - -
122C VAL* 1.3 82.7 - - - +
124C MET* 1.3 68.0 + - - +
125C GLY* 3.3 33.6 - - - -
126C GLU* 3.3 35.9 + - + +
490C GLN* 5.4 0.8 + - - -
493C ILE* 4.8 1.6 - - - +
495C ALA* 4.1 15.9 - - + +
499C SER* 5.7 0.5 + - - -
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Residues in contact with MET 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PHE* 3.6 21.5 - - + -
57C PHE* 5.8 4.9 - - + -
96C LEU* 3.1 27.0 + - + +
98C VAL* 3.3 37.7 - - + -
122C VAL* 4.4 4.9 - - + +
123C TYR* 1.3 78.0 - - - +
125C GLY* 1.3 65.1 + - - +
464C PHE* 4.9 1.3 - - + -
468C LEU* 4.7 7.2 - - + -
471C VAL* 6.3 0.4 - - - -
493C ILE* 4.4 23.8 - - + -
495C ALA* 3.6 19.3 - - - -
498C ILE* 3.4 41.6 - - + +
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Residues in contact with GLY 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LEU* 2.9 33.0 + - - +
123C TYR* 3.3 22.7 - - - -
124C MET* 1.3 72.4 - - - +
126C GLU* 1.3 61.7 + - - -
127C ILE* 5.0 1.8 - - - -
495C ALA* 3.8 4.5 - - - +
498C ILE* 5.3 1.6 - - - -
499C SER* 4.3 25.8 - - - -
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Residues in contact with GLU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 5.2 9.1 + - - +
93C SER* 2.5 43.0 + - - +
94C ALA 3.2 7.4 - - - +
95C PRO* 3.5 33.4 - - + +
123C TYR* 3.3 20.5 + - + +
125C GLY* 1.3 72.9 - - - -
127C ILE* 1.3 62.2 + - - +
128C PRO* 3.6 8.1 - - - +
499C SER* 5.1 8.1 + - - -
502C VAL* 5.1 4.2 - - - +
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 5.1 0.2 - - + -
38C PHE* 4.2 18.6 - - + -
39C ILE* 4.1 19.7 - - + -
49C LEU* 4.5 11.0 - - + -
75C LEU* 3.6 32.5 - - + -
93C SER* 3.6 1.6 - - - -
94C ALA 2.9 30.0 + - - +
96C LEU* 4.4 28.5 - - + -
125C GLY 4.7 1.6 - - - +
126C GLU* 1.3 75.4 - - - +
128C PRO* 1.3 72.7 - - + +
129C LEU* 3.9 5.4 - - + +
464C PHE* 5.6 6.5 - - + -
502C VAL* 5.1 9.6 - - + -
506C PHE* 6.3 0.7 - - + -
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Residues in contact with PRO 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 3.4 20.1 - - - -
91C THR* 4.3 8.3 - - + -
92C TYR 3.3 12.8 - - - +
93C SER* 3.8 3.1 - - - -
126C GLU 3.6 8.1 - - - +
127C ILE* 1.3 87.9 - - + +
129C LEU* 1.3 60.6 + - - +
136C PHE* 3.8 13.7 - - + -
138C ILE* 3.9 24.0 - - + -
502C VAL* 4.0 18.2 - - + -
503C LYS* 6.1 2.2 - - - -
506C PHE* 4.0 27.8 - - + -
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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