Contacts of the strand formed by residues 128 - 138 (chain C) in PDB entry 2XTJ
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 THR 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C GLN* 3.2 40.6 + - - +
124C LEU* 3.9 5.8 + - - -
126C SER* 3.9 3.5 + - - -
127C GLY* 1.3 82.4 - - - +
129C ALA* 1.3 63.2 + - - +
179C THR* 6.0 4.5 - - + -
180C LEU 4.2 8.5 - - - +
181C SER* 4.9 5.4 - - - -
182C LYS* 4.3 3.4 - - - +
161E LYS* 4.7 14.8 + - - +
162E ASP* 5.1 3.1 + - - -
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Residues in contact with ALA 129 (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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119C PRO* 3.7 20.0 - - + -
123C GLN* 3.6 1.6 - - - -
124C LEU* 3.8 13.5 - - + -
128C THR* 1.3 78.7 - - - +
130C SER* 1.3 64.9 + - - +
131C VAL* 4.2 1.3 - - - +
178C LEU 3.8 0.5 - - - +
179C THR* 3.7 4.0 + - - +
180C LEU* 3.1 39.2 + - + +
181C SER 4.7 2.0 - - - +
182C LYS 4.5 0.6 - - - +
185C TYR* 3.9 22.9 - - + -
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Residues in contact with SER 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PHE 4.1 0.3 - - - +
118C PRO 4.1 1.4 - - - +
119C PRO* 3.5 22.0 - - - +
123C GLN* 2.9 30.7 + - - +
129C ALA* 1.3 75.5 + - - +
131C VAL* 1.3 64.2 + - - +
132C VAL* 4.0 5.5 + - - +
177C THR* 4.0 16.8 - - - +
178C LEU 3.4 4.0 - - - -
179C THR* 4.1 6.1 + - - -
142E LEU* 5.9 1.0 - - - +
159E LEU* 3.8 16.6 - - - +
161E LYS* 3.3 20.6 - - - -
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Residues in contact with VAL 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 4.1 3.4 - - + -
117C PHE 3.4 15.5 - - - +
118C PRO* 4.7 0.2 - - + -
119C PRO* 4.0 15.7 - - + -
129C ALA 5.4 1.1 - - - -
130C SER* 1.3 75.6 - - - +
132C VAL* 1.3 61.2 + - - +
147C TRP* 3.6 30.2 - - + -
177C THR* 3.3 2.6 - - - -
178C LEU* 2.8 44.6 + - + +
180C LEU* 4.8 3.8 - - + -
185C TYR* 4.4 5.8 - - + -
191C TYR* 4.2 24.2 - - + -
208C PHE* 3.7 22.9 - - + -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 3.5 2.8 - - - +
117C PHE* 2.8 60.0 + - + -
130C SER 4.5 7.0 - - - +
131C VAL* 1.3 75.0 - - - +
133C CYS* 1.3 70.5 + - - +
134C LEU* 5.1 2.0 - - + -
147C TRP* 4.1 2.9 - - - -
175C SER* 4.8 10.8 - - - -
176C SER 3.3 7.6 - - - +
177C THR* 3.9 20.2 - - + +
142E LEU* 4.1 24.7 - - + -
159E LEU* 4.3 19.5 - - + -
197E SER* 5.2 3.8 - - - +
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Residues in contact with CYS 133 (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* 3.6 18.8 - - - -
115C PHE 3.5 6.5 - - - -
116C ILE* 4.6 1.3 - - - +
132C VAL* 1.3 77.0 - - - +
134C LEU* 1.3 62.5 + - - +
135C LEU* 3.9 9.6 - - + -
147C TRP* 3.6 17.9 - - + -
174C LEU 4.0 0.2 - - - +
175C SER* 3.4 3.3 - - - -
176C SER* 2.7 44.3 + - - +
193C CYS* 2.0 50.5 - - + -
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Residues in contact with LEU 134 (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 SER 3.4 1.0 - - - +
114C VAL* 3.3 5.7 - - - +
115C PHE* 2.7 61.7 + - + +
117C PHE* 4.2 13.9 - - + -
132C VAL* 5.1 2.9 - - + -
133C CYS* 1.3 74.2 - - - +
135C LEU* 1.3 76.6 + - - +
136C ASN* 3.9 19.5 - - - +
173C SER* 4.8 0.2 - - - -
174C LEU 3.5 10.3 - - - +
175C SER* 4.6 2.0 - - - +
155E ALA* 4.2 13.7 - - + -
184E PHE* 3.8 22.4 - - + -
199E VAL* 3.9 33.0 - - + -
201E THR* 5.8 0.4 - - + -
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Residues in contact with LEU 135 (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 PRO* 4.1 8.7 - - + -
113C SER 3.9 2.9 - - - -
114C VAL* 4.6 2.2 - - + -
133C CYS* 3.9 14.6 - - + -
134C LEU* 1.3 80.2 - - - +
136C ASN* 1.3 59.3 + - - +
138C PHE* 3.8 17.0 - - + -
143C ALA* 4.1 19.3 - - + -
145C VAL* 3.6 26.9 - - + -
173C SER* 3.2 7.1 - - - -
174C LEU* 2.7 55.3 + - + +
195C VAL* 3.5 46.7 - - + -
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Residues in contact with ASN 136 (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 ALA 4.4 0.3 - - - +
112C PRO* 3.5 2.5 - - - +
113C SER* 3.1 43.7 + - - +
115C PHE* 4.1 12.2 - - + -
134C LEU* 3.9 18.4 - - + +
135C LEU* 1.3 72.5 - - - +
137C ASN* 1.3 90.1 + - - +
138C PHE 3.4 1.9 + - - -
173C SER* 3.7 0.7 + - - -
182E HIS* 3.4 24.4 + - - -
199E VAL* 4.8 1.4 - - - +
201E THR* 3.6 31.3 + - - +
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Residues in contact with ASN 137 (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 ALA* 4.2 6.2 - - - +
111C ALA 4.1 7.4 - - - +
136C ASN* 1.3 90.2 + - - +
138C PHE* 1.3 59.0 + - - +
166C ASP* 4.8 0.6 + - - -
169C ASP* 3.4 28.2 + - - +
171C THR* 3.4 22.5 + - - +
172C TYR 3.2 6.9 + - - -
173C SER* 2.8 13.9 + - - -
182E HIS* 3.0 29.0 + - - -
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Residues in contact with PHE 138 (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 ALA 3.2 13.9 - - - +
112C PRO* 3.7 32.5 - - + -
135C LEU* 3.6 20.2 - - + -
137C ASN* 1.3 74.4 - - - +
139C TYR* 1.3 61.5 + - - +
140C PRO 3.3 19.1 - - - -
141C ARG* 3.3 29.6 - - - -
143C ALA* 3.9 14.1 - - + -
162C VAL* 5.0 2.9 - - + -
171C THR* 3.3 6.5 - - - -
172C TYR* 2.8 55.2 + - + +
173C SER 4.4 0.4 - - - -
174C LEU* 3.5 40.6 - - + -
197C HIS* 3.5 10.3 - + + -
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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