Contacts of the strand formed by residues 108 - 117 (chain C) in PDB entry 5I4A
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 ASN 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C TYR 3.6 1.0 - - - +
103C PHE* 3.7 2.1 - - - -
104C LYS* 2.8 55.6 + - + +
105C LYS 2.9 26.7 + - - -
106C GLY* 3.6 10.0 + - - -
107C ASN* 1.3 77.7 - - - +
109C PHE* 1.3 60.9 + - - +
110C ILE* 4.1 0.9 - - + -
129C THR* 4.0 11.7 - - + -
130C TYR 3.6 3.6 - - - -
131C LYS* 3.2 21.3 - - - +
148C LYS* 3.0 32.7 + - - +
150C THR* 5.8 0.7 - - - +
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TYR 5.7 0.2 - - - -
92C ILE* 4.4 3.8 - - + -
93C LYS* 3.8 28.7 - - + -
96C PHE* 3.4 57.2 - + + -
97C LEU* 5.4 1.6 - - + -
101C PHE* 3.7 9.3 - - + -
102C TYR 3.2 11.2 - - - -
103C PHE* 3.7 29.2 - + + -
107C ASN* 3.4 37.5 - - + -
108C ASN* 1.3 75.0 - - - +
110C ILE* 1.3 61.9 + - - +
111C SER 3.6 1.4 + - - -
129C THR* 3.3 6.0 - - - +
130C TYR 2.8 35.1 + - - +
132C ILE* 3.6 26.7 - - + -
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Residues in contact with ILE 110 (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 PHE* 3.4 3.5 - - - -
102C TYR* 2.7 44.3 + - + +
104C LYS* 3.8 31.4 - - + -
108C ASN* 5.2 0.2 - - + -
109C PHE* 1.3 72.8 - - - +
111C SER* 1.3 61.7 + - - +
112C ASN* 3.5 2.6 + - - -
127C HIS* 3.4 38.8 - - + +
129C THR* 3.8 10.1 - - + +
150C THR* 3.8 23.6 - - + +
152C LEU* 4.3 9.4 - - + -
168C TYR* 3.7 33.9 - - + +
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Residues in contact with SER 111 (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 PHE* 3.5 32.5 - - - -
110C ILE* 1.3 70.9 - - - +
112C ASN* 1.3 60.1 + - - +
113C SER* 3.2 7.6 + - - -
114C GLU* 2.9 38.2 + - - +
115C VAL* 3.3 5.2 - - - +
127C HIS* 3.0 26.7 + - - +
128C LEU* 2.9 25.3 + - - -
130C TYR* 5.9 0.2 - - - -
240C THR* 5.4 0.4 - - - -
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Residues in contact with ASN 112 (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 ASP* 3.1 38.0 + - + +
101C PHE* 5.6 0.4 - - - -
102C TYR* 3.4 53.0 + - - -
110C ILE 3.5 5.9 + - - -
111C SER* 1.3 74.1 + - - +
113C SER* 1.3 58.7 + - - +
115C VAL* 3.5 13.0 - - - +
127C HIS* 3.8 14.7 - - - -
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Residues in contact with SER 113 (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 PHE* 5.9 1.6 - - - -
111C SER* 3.2 6.5 + - - -
112C ASN* 1.3 78.1 - - - +
114C GLU* 1.3 78.9 + - - +
115C VAL* 3.2 11.1 + - - +
240C THR* 5.4 2.4 - - - +
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Residues in contact with GLU 114 (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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111C SER* 2.9 16.6 + - - +
113C SER* 1.3 89.4 + - - +
115C VAL* 1.3 60.8 + - - +
116C PHE* 5.3 3.5 - - - -
126C ALA 3.8 0.5 - - - +
128C LEU* 2.9 54.2 + - + +
149C PHE* 5.5 0.3 - - - -
236C LYS* 2.9 35.1 + - - +
240C THR* 4.1 17.0 + - + +
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Residues in contact with VAL 115 (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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111C SER 3.3 22.7 - - - +
112C ASN* 3.5 22.7 - - - +
113C SER 3.2 6.8 + - - +
114C GLU* 1.3 80.0 - - - +
116C PHE* 1.3 68.4 + - - +
125C ASN* 3.8 19.1 - - + +
126C ALA 3.2 12.3 - - - +
127C HIS* 3.4 33.9 - - + +
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Residues in contact with PHE 116 (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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114C GLU 5.3 2.5 - - - -
115C VAL* 1.3 78.9 - - - +
117C SER* 1.3 72.9 + - - +
118C LEU* 4.3 5.6 - - + -
119C ASP* 6.5 0.2 - - - -
125C ASN* 4.0 3.8 - - - -
126C ALA* 2.9 49.3 + - + +
149C PHE* 4.1 18.6 - + - -
221C GLU* 4.6 5.2 - - - -
225C ILE* 3.7 25.6 - - + -
229C LYS* 3.5 38.8 - - + -
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Residues in contact with SER 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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116C PHE* 1.3 83.0 - - - +
118C LEU* 1.3 66.5 + - - +
119C ASP* 3.5 6.9 + - - +
122C GLU* 2.8 55.2 + - - +
124C VAL 3.5 2.7 + - - -
125C ASN* 3.5 19.1 - - - +
154C LYS* 4.6 5.2 - - - -
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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