Contacts of the strand formed by residues 131 - 140 (chain L) in PDB entry 4XX1
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 ALA 131 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L PRO* 4.2 17.0 - - + -
125L GLU* 3.1 5.4 - - - -
126L LEU* 4.4 1.1 - - + -
130L LYS* 1.3 77.6 - - - +
132L THR* 1.3 61.1 + - - +
133L LEU* 5.8 1.6 - - + -
179L LEU 3.5 0.7 - - - +
180L SER* 3.4 5.4 - - - -
181L LEU* 2.6 53.7 + - + +
182L THR 4.2 0.4 - - - +
183L PRO* 3.7 25.8 - - + +
186L TRP* 5.2 3.1 - - + -
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Residues in contact with THR 132 (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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135H PHE* 4.2 5.6 - - + -
154H LEU* 3.6 27.0 - - + +
157H ASP* 6.1 0.9 - - - +
120L PRO 4.2 1.4 - - - +
121L PRO* 3.3 24.5 - - - +
122L SER 5.3 0.7 + - - -
125L GLU* 2.7 43.2 + - - +
130L LYS* 6.0 2.0 - - + -
131L ALA* 1.3 76.7 - - - +
133L LEU* 1.3 63.3 + - - +
134L VAL* 4.1 3.9 + - - +
178L TYR* 5.9 4.3 - - + -
179L LEU 3.2 6.3 - - - +
180L SER* 5.0 7.9 - - - -
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Residues in contact with LEU 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L LEU* 4.8 5.8 - - + -
119L PHE 3.2 20.0 - - - +
120L PRO* 3.9 2.5 - - + -
121L PRO* 3.5 30.1 - - + -
131L ALA* 5.8 1.1 - - + -
132L THR* 1.3 73.4 - - - +
134L VAL* 1.3 62.3 + - - +
135L CYS 3.6 1.0 + - - -
149L TRP* 3.9 13.3 - - + -
178L TYR* 3.2 10.1 - - - +
179L LEU* 2.8 51.4 + - + +
181L LEU* 5.6 2.0 - - + -
186L TRP* 4.3 11.9 - - + +
192L TYR* 3.5 44.2 - - + -
207L VAL* 5.5 4.7 - - + -
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Residues in contact with VAL 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H LEU* 4.0 16.2 - - + -
154H LEU* 3.7 35.9 - - + -
192H SER* 3.9 10.1 - - - +
117L THR 3.9 0.5 - - - +
118L LEU* 3.2 6.1 - - - +
119L PHE* 2.9 50.2 + - + -
120L PRO 5.8 1.1 - - - +
132L THR* 4.1 4.9 + - - +
133L LEU* 1.3 72.5 - - - +
135L CYS* 1.3 60.1 + - - +
136L LEU* 3.8 22.4 - - + -
178L TYR* 3.6 24.5 - - + -
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Residues in contact with CYS 135 (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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116L VAL* 3.7 20.0 - - - -
117L THR 3.5 4.7 - - - -
118L LEU* 4.1 3.6 - - - -
133L LEU 3.6 0.6 + - - -
134L VAL* 1.3 73.6 - - - +
136L LEU* 1.3 61.7 + - - +
137L ILE* 4.0 6.4 + - - +
147L VAL* 5.8 2.0 - - - -
149L TRP* 3.8 6.1 - - + -
176L SER* 3.8 2.8 - - - -
177L SER* 3.2 43.9 + - - +
178L TYR* 3.7 0.7 - - - -
194L CYS* 2.0 53.2 - - - -
196L VAL* 5.7 2.5 - - - -
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Residues in contact with LEU 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H LEU* 5.3 0.4 - - + -
179H PHE* 3.7 40.2 - - + -
192H SER* 3.9 13.2 - - - +
194H VAL* 3.8 30.7 - - + -
115L SER 3.7 2.3 - - - +
116L VAL* 3.4 3.8 - - - -
117L THR* 2.8 44.7 + - - +
119L PHE* 4.3 9.4 - - + -
134L VAL* 3.8 16.8 - - + +
135L CYS* 1.3 72.4 - - - +
137L ILE* 1.3 63.2 + - - +
138L SER* 5.0 0.3 + - - -
175L ALA 3.9 0.7 - - - -
176L SER* 4.2 3.6 - - - +
178L TYR* 3.4 32.8 - - + +
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Residues in contact with ILE 137 (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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179H PHE* 3.0 10.4 - - - -
114L PRO* 3.5 31.0 - - + -
115L SER 4.3 1.6 - - - -
116L VAL* 4.0 16.2 - - + +
135L CYS* 4.7 7.0 - - - +
136L LEU* 1.3 75.8 - - - +
138L SER* 1.3 62.6 + - - +
140L PHE* 3.5 13.7 - - + -
145L VAL* 3.7 11.0 - - + -
147L VAL* 3.7 18.6 - - + -
162L THR* 5.1 0.9 - - + -
175L ALA* 2.6 52.4 + - + +
176L SER* 5.2 0.4 - - - +
177L SER* 5.5 2.0 - - - +
196L VAL* 3.6 28.0 - - + -
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Residues in contact with SER 138 (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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177H HIS* 3.8 21.5 - - - -
179H PHE* 3.8 21.2 - - - -
114L PRO* 3.8 1.9 - - - +
115L SER* 3.0 39.4 + - - +
136L LEU 5.0 0.2 + - - -
137L ILE* 1.3 78.7 - - - +
139L ASP* 1.3 73.3 + - - +
140L PHE* 3.6 2.9 + - - -
173L TYR 3.5 8.5 - - - -
174L ALA* 3.8 3.1 - - - +
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Residues in contact with ASP 139 (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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177H HIS* 4.3 11.1 + - - -
112L ALA* 4.1 4.3 - - - +
113L ALA 3.3 16.8 - - - +
115L SER* 4.6 12.0 - - - -
138L SER* 1.3 87.1 + - - +
140L PHE* 1.3 56.4 + - - +
170L ASN* 2.8 29.1 + - - +
172L LYS* 3.8 17.0 + - - +
173L TYR 2.8 12.5 + - - -
174L ALA* 4.9 0.2 - - - +
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Residues in contact with PHE 140 (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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112L ALA 3.2 11.4 - - - +
114L PRO* 3.6 21.5 - - + -
137L ILE* 3.5 29.2 - - + -
138L SER 3.8 6.5 - - - -
139L ASP* 1.3 75.4 - - - +
141L TYR* 1.3 60.3 + - - +
142L PRO 3.8 3.6 - - - -
143L GLY* 3.6 28.5 - - - -
145L VAL* 3.5 27.6 - - + -
165L PRO* 4.5 5.8 - - + -
172L LYS* 3.2 13.1 - - - +
173L TYR* 3.4 44.5 + - + -
174L ALA* 3.6 21.8 - - - -
175L ALA* 4.1 8.3 - - + -
198L HIS* 3.9 1.6 - - - +
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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