Contacts of the strand formed by residues 130 - 140 (chain B) in PDB entry 6PI7
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 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B GLN* 3.2 44.5 + - - +
126B LEU* 3.7 6.1 + - - -
128B SER* 3.7 7.8 + - - -
129B GLY* 1.3 79.8 + - - +
131B ALA* 1.3 66.4 + - - +
181B THR* 4.1 18.2 - - + -
182B LEU 3.5 14.8 + - - +
183B SER* 5.1 1.6 - - - -
184B LYS* 4.2 4.5 - - - +
157C LYS* 5.4 4.9 - - + -
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B PRO* 4.0 20.4 - - + -
125B GLN* 3.8 4.0 - - - -
126B LEU* 6.1 1.8 - - + -
130B THR* 1.3 75.8 - - - +
132B SER* 1.3 59.0 + - - +
133B VAL* 5.0 4.8 - - + +
180B LEU 3.7 1.4 - - - +
181B THR* 3.5 3.3 - - - -
182B LEU* 2.9 43.5 + - + +
183B SER 4.6 1.3 - - - +
184B LYS* 4.6 1.5 - - - +
187B TYR* 3.7 29.8 - - + -
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO 4.1 1.9 - - - +
121B PRO* 3.4 22.1 - - - +
125B GLN* 3.0 27.6 + - - +
131B ALA* 1.3 70.2 - - - +
133B VAL* 1.3 60.8 + - - +
134B VAL* 4.3 1.5 + - - +
179B THR* 4.1 18.8 - - - -
180B LEU 3.5 5.4 - - - -
181B THR* 4.7 5.4 - - - +
155C LEU* 5.1 14.6 - - - -
157C LYS* 5.4 4.3 - - - -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 4.1 3.6 - - + -
119B PHE 3.5 15.5 - - - +
121B PRO* 4.2 16.6 - - + -
131B ALA* 5.0 5.8 - - + +
132B SER* 1.3 76.8 - - - +
134B VAL* 1.3 59.6 - - - +
149B TRP* 3.6 29.4 - - + -
179B THR* 3.3 5.6 - - - +
180B LEU* 2.9 42.0 + - + +
182B LEU* 6.3 2.0 - - + -
187B TYR* 6.5 0.2 - - + -
193B TYR* 4.9 7.6 - - + -
210B PHE* 3.6 24.7 - - + -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 3.3 4.9 - - - +
119B PHE* 2.8 57.6 + - + -
132B SER* 4.2 1.5 + - - +
133B VAL* 1.3 73.6 - - - +
135B CYS* 1.3 59.3 + - - +
136B LEU 4.2 0.2 - - - -
149B TRP* 4.0 3.1 - - - -
177B SER* 6.1 4.0 - - - -
178B SER 3.4 6.1 - - - +
179B THR* 4.6 9.2 - - + +
138C LEU* 6.0 2.2 - - + -
193C SER* 5.1 10.8 - - - +
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Residues in contact with CYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL* 5.7 3.1 - - + -
117B PHE 3.4 7.9 - - - +
118B ILE* 4.5 0.4 - - - +
134B VAL* 1.3 72.7 - - - +
136B LEU* 1.3 59.6 + - - +
137B LEU 4.2 0.4 + - - -
149B TRP* 3.7 20.6 - - + -
176B LEU 4.0 0.7 - - - +
177B SER* 3.3 5.8 - - - -
178B SER* 2.8 42.6 + - - +
195B CYS* 3.7 23.1 - - + -
197B VAL* 5.8 4.7 - - + -
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B SER 3.2 7.3 - - - +
116B VAL* 3.4 4.5 - - - +
117B PHE* 2.8 49.3 + - + +
119B PHE* 4.0 19.5 - - + -
134B VAL 4.2 0.4 - - - -
135B CYS* 1.3 71.9 - - - +
137B LEU* 1.3 59.4 + - - +
138B ASN* 4.5 14.6 - - + +
175B SER* 6.2 0.2 - - - -
176B LEU 3.7 5.8 - - - +
177B SER* 4.7 3.4 - - - +
197B VAL* 6.4 0.2 - - - -
151C ALA* 5.4 2.7 - - + -
180C PHE* 5.1 5.4 - - + -
195C VAL* 4.4 29.2 - - + -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PRO* 3.9 22.2 - - + -
115B SER 3.7 4.5 - - - -
116B VAL* 4.8 1.8 - - + +
135B CYS 4.2 0.8 + - - -
136B LEU* 1.3 69.9 - - - +
138B ASN* 1.3 60.1 + - - +
140B PHE* 5.5 2.5 - - + +
145B ALA* 6.1 4.7 - - + -
174B TYR 4.4 0.3 - - - +
175B SER* 3.2 6.9 - - - -
176B LEU* 2.8 48.3 + - + +
197B VAL* 5.1 14.1 - - + -
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Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA 4.5 0.2 - - - +
114B PRO* 3.6 1.7 - - - +
115B SER* 3.0 39.1 + - - +
117B PHE* 3.9 15.9 - - + -
136B LEU* 4.5 11.5 - - + +
137B LEU* 1.3 71.0 - - - +
139B ASN* 1.3 88.7 + - - +
140B PHE 3.6 0.4 - - - -
175B SER* 3.7 6.3 - - - -
176C GLY 5.0 0.2 + - - -
178C HIS* 3.2 29.0 - - - -
195C VAL* 4.8 4.9 - - - +
197C THR* 2.9 31.3 + - - +
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA* 4.4 5.7 - - - +
113B ALA 3.8 9.4 - - - +
138B ASN* 1.3 93.7 + - - +
140B PHE* 1.3 58.5 + - - +
171B ASP* 4.4 10.2 + - - +
173B THR* 3.4 30.8 + - + +
174B TYR 3.1 14.0 + - - +
175B SER* 4.1 1.3 - - - -
176C GLY* 6.3 1.4 - - - -
178C HIS* 3.0 29.2 + - - -
197C THR* 5.0 2.2 + - - +
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA* 3.2 15.7 - - - +
114B PRO* 3.6 31.9 - - + -
137B LEU* 5.5 2.5 - - + +
138B ASN 4.9 0.2 - - - -
139B ASN* 1.3 74.8 - - - +
141B TYR* 1.3 63.0 + - - +
142B PRO 4.4 3.1 - - - +
173B THR* 3.5 3.2 - - - -
174B TYR* 2.8 40.3 + - + +
199B HIS* 4.1 10.1 - - + +
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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