Contacts of the strand formed by residues 121 - 126 (chain C) in PDB entry 1XXB
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 ILE 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C LEU* 3.5 46.7 - - + +
113C ASP* 6.0 0.2 - - - +
115C LEU* 3.6 26.2 - - + -
116C GLY* 3.2 12.5 + - - +
117C LYS* 3.1 22.0 + - - +
119C GLU 4.9 0.4 - - - +
120C GLY* 1.3 74.5 - - - +
122C LEU* 1.3 63.4 + - - +
123C GLY* 3.4 19.1 - - - +
124C THR* 3.5 7.6 - - - +
133C THR* 3.3 20.6 - - - +
134C THR 3.8 2.9 - - - +
136C ALA* 4.7 0.2 - - - -
144C LEU* 3.6 21.1 - - + -
147C ALA* 6.2 0.2 - - + -
148C ILE* 4.5 1.3 - - + -
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Residues in contact with LEU 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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88B ASP* 5.7 0.2 - - - +
90B ASP* 3.4 36.6 - - + +
91B TYR* 3.6 32.3 - - - +
92B ASN* 4.0 13.9 - - + +
97B VAL* 3.6 28.9 - - + +
99B HIS* 3.2 19.9 + - + +
117C LYS* 3.8 16.2 - - + -
120C GLY 3.8 2.4 + - - -
121C ILE* 1.3 75.0 - - - +
123C GLY* 1.3 59.0 + - - +
134C THR* 2.8 18.7 + - + +
135C PRO 3.8 6.7 - - - +
136C ALA* 4.0 16.5 - - + +
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Residues in contact with GLY 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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97B VAL* 3.9 17.9 - - - -
99B HIS* 4.3 9.4 - - - -
132B PHE* 3.6 7.4 - - - -
113C ASP* 5.3 0.9 - - - -
121C ILE* 3.3 4.5 - - - +
122C LEU* 1.3 82.4 - - - +
124C THR* 1.3 67.5 + - - -
133C THR* 3.3 3.1 + - - -
134C THR* 3.2 24.2 + - - +
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Residues in contact with THR 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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130B THR* 3.1 29.0 + - - +
132B PHE* 3.6 4.6 - - - -
1C ARG* 3.4 7.5 + - - -
109C ALA* 4.2 14.4 - - + -
112C LEU* 3.9 20.7 - - + +
113C ASP* 3.8 19.7 + - - -
121C ILE* 3.5 9.0 - - - +
123C GLY* 1.3 78.7 + - - -
125C ILE* 1.3 65.9 + - - +
131C ILE* 3.6 26.9 - - + -
132C PHE 3.6 6.1 - - - +
133C THR* 3.3 11.4 + - - +
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Residues in contact with ILE 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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125A ILE* 3.1 37.1 - - + +
125B ILE* 3.1 39.0 - - + +
126B ALA 5.8 0.2 - - - -
127B GLY* 4.4 8.1 - - - +
130B THR* 3.7 18.4 - - + +
132B PHE* 3.4 38.1 - - + +
1C ARG 3.9 2.7 - - - +
124C THR* 1.3 79.1 - - - +
126C ALA* 1.3 62.1 + - - +
131C ILE* 3.1 3.9 - - - +
132C PHE* 2.7 44.7 + - + +
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Residues in contact with ALA 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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125A ILE* 4.6 5.8 - - - +
126A ALA 5.3 0.5 - - - +
127B GLY* 4.6 6.6 - - - -
1C ARG 3.2 9.9 + - - +
105C ALA* 3.7 21.3 - - + +
106C GLN* 3.2 26.4 + - - +
109C ALA* 3.6 29.4 - - + -
125C ILE* 1.3 75.5 - - - +
127C GLY* 1.3 60.3 + - - +
130C THR 3.4 5.4 - - - +
131C ILE* 4.2 2.9 - - + +
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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