Contacts of the strand formed by residues 103 - 116 (chain C) in PDB entry 2XN9
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 LYS 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C GLU* 4.2 12.9 + - - -
72C ASP* 2.4 32.8 + - - -
99C LEU 4.6 1.8 - - - -
100C ASN* 3.3 33.6 + - - +
101C SER 2.9 10.1 + - - +
102C GLU* 1.3 80.3 - - - +
104C LEU* 1.3 68.3 + - - +
105C ALA 4.0 0.2 + - - -
129C ASN* 3.4 38.8 - - + +
130C LYS* 4.3 11.2 - - - +
131C LYS* 4.3 5.6 - - - +
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Residues in contact with LEU 104 (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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103C LYS* 1.3 82.0 - - - +
105C ALA* 1.3 64.2 + - - +
106C GLN 3.3 19.9 - - - +
108C ARG* 3.6 30.7 - - + -
128C THR 3.7 10.8 - - - +
129C ASN* 2.9 14.8 + - - +
130C LYS 3.7 13.7 - - - +
131C LYS* 3.6 30.7 - - + +
200C LYS* 6.3 0.7 - - - -
201C SER* 4.1 6.5 - - - -
202C ASP* 4.2 22.4 - - - +
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Residues in contact with ALA 105 (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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104C LEU* 1.3 75.2 - - - +
106C GLN* 1.3 67.7 + - + +
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Residues in contact with GLN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 3.4 19.2 - - - +
105C ALA* 1.3 85.4 - - + +
107C GLU* 1.3 73.8 + - - +
108C ARG* 3.3 2.8 + - - -
129C ASN* 5.6 0.9 - - - -
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Residues in contact with GLU 107 (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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106C GLN* 1.3 83.1 - - - +
108C ARG* 1.3 64.6 + - - +
109C VAL* 3.7 11.3 + - + +
127C ARG* 3.4 55.5 + - + +
128C THR* 3.9 14.9 + - - +
129C ASN* 4.7 11.6 - - + +
69E GLU* 5.0 0.3 - - - +
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Residues in contact with ARG 108 (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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104C LEU* 3.6 20.4 - - + -
106C GLN 3.3 2.2 + - - -
107C GLU* 1.3 72.6 - - - +
109C VAL* 1.3 85.3 + - - +
110C ILE* 4.0 22.4 + - + +
127C ARG* 3.3 5.4 - - - +
128C THR* 2.9 43.0 + - + +
169C LYS* 4.9 3.4 - - - +
201C SER* 3.5 26.5 + - - +
202C ASP* 5.0 8.4 + - - +
204C ILE* 2.4 33.7 + - - +
205C SER 3.1 17.6 + - - -
73E ALA* 5.4 6.1 - - - +
76E ASP* 4.1 12.5 + - - +
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLU* 3.7 12.5 + - + +
108C ARG* 1.3 104.5 + - - +
110C ILE* 1.3 59.2 + - - +
111C GLY 4.2 0.7 + - - -
125C LEU* 4.0 30.5 - - + -
126C ILE 3.5 10.5 - - - +
127C ARG* 4.3 13.7 - - + +
69E GLU* 4.3 33.7 - - + +
73E ALA* 4.5 9.8 - - + +
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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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108C ARG* 4.0 29.4 - - + +
109C VAL* 1.3 79.7 - - - +
111C GLY* 1.3 71.8 + - - +
112C ALA* 5.3 0.9 - - - +
125C LEU* 3.7 1.4 - - - -
126C ILE* 2.9 43.3 + - + +
128C THR* 4.8 7.9 - - + +
138C LEU* 4.2 23.8 - - + -
204C ILE* 3.8 46.4 - - + -
205C SER 4.5 2.7 - - - +
206C HIS* 4.1 9.9 - - - -
207C ILE* 4.2 15.0 - - + -
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Residues in contact with GLY 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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109C VAL 4.2 1.2 + - - -
110C ILE* 1.3 75.9 - - - +
112C ALA* 1.3 61.6 + - - +
123C THR* 4.9 1.1 - - - -
124C GLU 3.4 8.3 - - - -
125C LEU* 4.0 10.3 - - - -
205C SER 5.2 1.0 + - - -
206C HIS* 3.6 7.2 - - - +
207C ILE* 3.0 22.3 + - - +
73E ALA* 4.3 8.8 - - - +
77E THR* 3.5 24.0 - - - +
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Residues in contact with ALA 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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110C ILE 5.3 0.9 - - - +
111C GLY* 1.3 74.6 - - - +
113C ASN* 1.3 65.4 + - - +
114C VAL* 4.0 2.3 - - + +
123C THR* 3.3 8.7 - - - +
124C GLU* 2.8 49.6 + - + +
125C LEU* 5.7 0.4 - - - -
142C ILE* 4.1 17.5 - - + -
207C ILE* 3.2 27.6 - - + +
209C VAL* 4.8 4.9 - - + -
77E THR* 4.1 0.8 - - - +
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Residues in contact with ASN 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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112C ALA* 1.3 74.6 - - - +
114C VAL* 1.3 63.1 + - - +
115C TRP* 3.7 15.9 - - + -
120C GLN* 6.1 1.7 - - + -
123C THR* 4.4 12.3 + - - +
206C HIS* 3.6 13.7 + - - -
207C ILE 2.9 6.3 + - - -
208C ASP* 3.0 24.1 + - - +
209C VAL* 2.8 28.4 + - - +
77E THR* 2.8 41.8 + - - +
81E HIS* 4.0 0.4 + - - -
4F VAL* 3.6 25.0 - - - +
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Residues in contact with VAL 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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112C ALA* 3.9 4.7 + - + +
113C ASN* 1.3 83.0 - - - +
115C TRP* 1.3 70.0 + - - +
116C VAL* 4.5 2.7 - - + -
120C GLN* 3.7 6.6 - - - +
121C LYS* 2.8 38.0 + - + +
122C GLU 3.9 20.5 + - - +
123C THR* 5.2 0.4 - - - +
124C GLU* 4.0 21.5 - - + -
146C LEU* 4.8 5.4 - - + -
150C TYR* 3.9 30.5 - - + +
209C VAL* 3.4 27.1 - - + +
211C LEU* 4.8 2.0 - - + -
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Residues in contact with TRP 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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113C ASN* 3.7 20.0 - - + -
114C VAL* 1.3 74.9 - - - +
116C VAL* 1.3 61.8 + - - +
117C ASP 4.1 0.4 - - - -
118C GLY* 3.2 31.4 - - - -
119C ILE 3.2 4.9 - - - +
120C GLN* 3.5 35.3 + - + +
208C ASP* 3.7 27.6 - - + -
209C VAL 2.9 22.6 + - - +
210C ASN* 3.4 28.8 - - - +
211C LEU* 2.8 32.9 + - - +
81E HIS* 4.0 9.9 - + - -
2F LYS* 3.5 32.6 - - + +
3F TYR 4.5 5.6 + - - -
4F VAL* 3.6 28.5 - - + -
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Residues in contact with VAL 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 VAL* 4.5 1.8 - - + -
115C TRP* 1.3 78.0 - - - +
117C ASP* 1.3 71.8 + - - +
119C ILE* 2.9 34.1 + - - +
121C LYS* 3.8 31.1 - - + -
150C TYR* 4.1 14.1 - - + -
158C GLU* 5.4 4.3 - - - +
159C ILE* 4.0 20.6 - - + -
211C LEU* 3.3 29.2 - - + +
213C THR* 4.2 14.1 - - - +
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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