Contacts of the strand formed by residues 153 - 161 (chain L) in PDB entry 2I2X
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 153 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122L THR* 3.4 25.0 + - + +
124L GLY 3.0 12.7 + - - +
125L THR* 3.3 23.9 + - - +
126L VAL* 3.0 25.5 + - - +
152L TYR* 1.3 70.7 - - - +
154L VAL* 1.3 67.4 + - - +
155L VAL* 5.0 1.4 + - - +
173L GLU* 5.0 4.0 - - - +
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Residues in contact with VAL 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L VAL* 3.6 6.7 - - + +
128L CYS* 3.7 20.0 - - + -
144L THR* 3.7 24.2 - - - +
147L LEU* 3.5 36.6 - - + -
148L ARG* 3.6 45.1 + - + +
152L TYR 3.7 5.5 + - - +
153L ASN* 1.3 86.0 + - - +
155L VAL* 1.3 68.7 + - - +
156L ASP* 3.8 1.2 + - - +
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Residues in contact with VAL 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L THR* 4.3 7.0 - - + -
126L VAL 3.4 7.1 + - - +
127L VAL* 3.7 29.3 - - + -
128L CYS 3.2 25.3 + - - -
153L ASN* 4.0 3.1 + - - +
154L VAL* 1.3 72.6 - - - +
156L ASP* 1.3 62.1 + - - +
157L LEU* 3.7 19.4 + - + +
169L ALA* 5.7 2.7 - - + -
173L GLU* 4.0 27.6 - - + +
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Residues in contact with ASP 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L CYS* 3.9 2.9 - - - -
140L LYS* 3.3 32.5 + - - +
141L ASN* 4.1 3.5 - - - +
144L THR* 3.4 27.1 + - - +
148L ARG* 4.2 17.0 + - - +
154L VAL* 3.8 3.6 + - + -
155L VAL* 1.3 73.3 - - - +
157L LEU* 1.3 62.6 + - - +
158L GLY* 3.0 17.5 + - - -
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Residues in contact with LEU 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K ARG* 4.1 12.6 + - - -
127L VAL* 3.7 29.8 - - + -
128L CYS 3.0 16.3 + - - +
129L HIS* 3.9 4.7 - - + -
155L VAL* 3.9 21.1 - - + +
156L ASP* 1.3 70.3 - - - +
158L GLY* 1.3 57.0 + - - +
159L ARG 4.0 0.5 + - - -
161L VAL* 3.3 34.7 - - + +
165L GLU* 3.6 46.7 - - + +
166L VAL* 5.1 2.5 - - - -
169L ALA* 4.1 10.8 - - + -
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Residues in contact with GLY 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K ARG* 5.0 0.7 - - - -
128L CYS 4.4 0.2 + - - -
129L HIS* 4.3 0.2 - - - -
130L VAL 3.7 5.9 + - - -
140L LYS* 3.4 35.0 + - - +
156L ASP* 3.0 11.4 + - - -
157L LEU* 1.3 78.9 - - - +
159L ARG* 1.3 65.6 + - - +
161L VAL* 3.6 5.5 - - - +
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Residues in contact with ARG 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K GLU* 2.5 33.2 + - - +
132K ASN 3.2 19.4 + - - -
133K ARG* 3.2 20.5 + - - +
134K GLU 3.5 21.0 + - - -
135K PHE* 4.5 3.6 - - - +
136K LEU 5.5 0.2 - - - +
169K LYS* 5.5 0.6 - - - +
453K VAL* 5.2 7.5 - - - +
130L VAL* 2.7 26.2 - - + +
134L ASP 3.7 15.4 - - - +
135L VAL* 3.3 27.1 - - + +
137L ASP* 3.2 37.2 + - - +
140L LYS* 4.7 0.2 - - - +
157L LEU 4.0 1.2 + - - -
158L GLY* 1.3 71.5 - - - +
160L ASP* 1.3 56.0 + - + +
161L VAL* 2.4 25.1 + - - +
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Residues in contact with ASP 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K ARG* 3.6 44.1 + - + +
132L GLU* 3.4 9.2 - - - +
133L GLY* 2.8 31.4 + - - -
134L ASP 4.0 9.2 - - - +
135L VAL* 5.4 5.5 - - + +
159L ARG* 1.3 73.4 - - + +
161L VAL* 1.3 61.8 + - - +
162L PRO* 3.2 14.6 - - - +
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Residues in contact with VAL 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K ARG* 4.3 3.1 - - - +
129L HIS* 3.8 17.0 - - + -
130L VAL 3.3 10.8 + - - +
131L ALA* 4.0 0.3 - - - -
132L GLU* 3.4 17.7 + - - +
157L LEU* 3.3 52.0 - - + +
158L GLY 3.6 10.8 - - - +
159L ARG 2.4 31.7 + - - +
160L ASP 1.3 63.2 - - - +
162L PRO* 1.3 68.7 - - + +
163L ALA 3.3 6.4 + - - -
165L GLU* 4.4 2.5 - - + +
166L VAL* 3.5 25.6 - - + -
190L ALA* 5.6 0.3 - - - +
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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