Contacts of the strand formed by residues 133 - 142 (chain L) in PDB entry 6D2P
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 133 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L PRO* 3.9 23.1 - - + -
127L GLU* 3.6 3.8 - - - -
128L LEU* 4.2 10.1 - - + -
132L LYS* 1.3 80.1 - - - +
134L THR* 1.3 63.8 + - - +
182L SER* 3.6 1.6 - - - -
183L LEU* 2.6 57.9 + - + +
184L THR 4.4 0.4 - - - -
185L PRO* 4.3 9.6 - - + -
188L TRP* 4.5 3.8 - - + -
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Residues in contact with THR 134 (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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146H LEU* 4.2 13.2 - - + +
148H LYS* 3.4 22.7 + - + -
122L PRO 4.1 2.3 - - - +
123L PRO* 3.5 22.5 - - - +
124L SER 4.8 0.2 + - - -
127L GLU* 2.6 31.3 + - - +
132L LYS* 5.7 0.3 - - - +
133L ALA* 1.3 75.0 + - - +
135L LEU* 1.3 74.0 + - - +
136L VAL* 3.9 18.8 + - + +
180L TYR* 4.2 16.2 - - + -
181L LEU 3.8 7.2 - - - +
182L SER* 4.2 7.1 + - - +
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Residues in contact with LEU 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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120L LEU* 4.4 2.5 - - + -
121L PHE 3.4 15.9 - - - +
123L PRO* 3.6 22.2 - - + -
133L ALA 4.4 0.2 - - - -
134L THR* 1.3 75.5 - - - +
136L VAL* 1.3 60.0 + - - +
137L CYS 4.1 0.7 - - - -
151L TRP* 3.7 20.1 - - + -
179L SER 3.9 0.7 - - - +
180L TYR* 3.4 7.6 - - - -
181L LEU* 3.0 55.0 + - + +
183L LEU* 3.8 13.7 - - + -
188L TRP* 3.8 3.1 - - + -
194L TYR* 3.7 33.7 - - + -
209L VAL* 3.8 23.1 - - + -
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Residues in contact with VAL 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H LEU* 4.5 10.5 - - + -
146H LEU* 3.8 30.5 - - + -
184H SER* 3.7 12.8 - - - +
119L THR 3.4 5.0 - - - +
120L LEU* 3.9 2.2 - - - +
121L PHE* 2.8 51.2 + - + +
134L THR* 4.0 10.5 - - + +
135L LEU* 1.3 77.6 - - - +
137L CYS* 1.3 59.3 + - - +
138L LEU* 3.7 32.8 - - + -
179L SER 4.0 1.6 - - - -
180L TYR* 3.9 13.5 - - + -
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Residues in contact with CYS 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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118L VAL* 3.7 23.1 - - - -
119L THR 3.7 2.9 - - - -
120L LEU* 4.1 3.1 - - + -
135L LEU 4.1 0.8 + - - -
136L VAL* 1.3 72.4 - - - +
138L LEU* 1.3 60.9 + - - +
139L ILE* 4.0 6.8 + - - +
149L VAL* 4.9 0.2 - - - -
151L TRP* 3.8 7.4 - - + -
178L SER* 3.3 6.9 - - - -
179L SER* 2.9 45.1 + - - +
196L CYS* 2.0 50.3 - - + -
198L VAL* 4.2 7.6 - - - -
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Residues in contact with LEU 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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129H LEU* 4.9 2.2 - - + -
171H PHE* 3.7 26.0 - - + -
184H SER* 4.1 15.5 - - - -
186H VAL* 3.6 36.1 - - + +
117L SER 3.2 5.5 - - - +
118L VAL* 3.5 1.6 - - - -
119L THR* 2.9 41.8 + - - +
121L PHE* 3.9 18.4 - - + -
136L VAL* 3.7 24.9 - - + -
137L CYS* 1.3 73.7 - - - +
139L ILE* 1.3 61.8 + - - +
140L SER* 5.5 0.2 - - - -
177L ALA 4.1 0.2 - - - -
178L SER* 3.7 24.0 - - - -
180L TYR* 4.8 0.2 - - - +
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Residues in contact with ILE 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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171H PHE* 3.2 8.2 - - - -
116L PRO* 3.6 27.6 - - + -
117L SER 3.5 3.4 - - - +
118L VAL* 4.5 3.4 - - + -
137L CYS* 4.2 11.9 - - - +
138L LEU* 1.3 76.8 - - - +
140L SER* 1.3 63.9 + - - +
142L PHE* 3.8 13.0 - - + -
147L VAL* 4.9 2.7 - - + -
149L VAL* 3.7 24.0 - - + -
176L ALA* 3.3 1.0 - - - -
177L ALA* 2.8 58.0 + - + +
178L SER* 4.7 2.9 - - - +
179L SER 5.1 0.7 - - - +
198L VAL* 3.7 38.1 - - + -
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Residues in contact with SER 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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169H HIS* 4.2 15.5 - - - -
171H PHE* 4.4 6.5 - - - -
116L PRO* 3.4 1.7 - - - +
117L SER* 2.7 48.4 + - - -
138L LEU 5.5 0.4 - - - -
139L ILE* 1.3 77.3 - - - +
141L ASP* 1.3 80.1 + - - +
142L PHE* 3.5 2.9 - - - -
170L GLN* 3.2 14.1 - - - -
175L TYR 3.8 2.5 - - - -
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Residues in contact with ASP 141 (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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114L ALA* 4.2 1.6 - - - +
115L ALA 3.0 19.6 - - - +
117L SER* 4.0 12.5 + - - +
140L SER* 1.3 80.9 + - - +
142L PHE* 1.3 57.4 + - - +
170L GLN* 2.4 48.8 + - - -
172L ASN* 3.9 13.6 + - - -
174L LYS* 3.7 33.1 + - - +
175L TYR 3.2 0.2 + - - -
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Residues in contact with PHE 142 (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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114L ALA* 3.5 11.4 - - - +
116L PRO* 3.6 31.4 - - + -
139L ILE* 3.8 17.9 - - + -
140L SER 4.1 3.4 - - - -
141L ASP* 1.3 77.6 - - - +
143L TYR* 1.3 62.3 + - - +
144L PRO 3.4 11.4 - - - -
145L GLY* 3.9 12.3 - - - -
146L ALA 4.0 1.1 - - - -
147L VAL* 3.6 28.9 - - + -
167L PRO* 4.1 5.4 - - + -
174L LYS* 4.2 1.3 - - - -
175L TYR* 2.9 70.2 + - + +
176L ALA* 3.5 16.8 - - - -
177L ALA 3.8 2.0 - - - -
200L HIS* 3.5 13.9 - + + +
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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