Contacts of the strand formed by residues 122 - 131 (chain B) in PDB entry 3LPK
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 ARG 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B THR 3.9 2.2 - - - +
121B TYR* 1.3 83.1 - - - +
123B ASP* 1.3 62.1 + - - +
124B LEU* 3.6 2.7 + - + +
142B GLY* 3.0 5.9 - - - -
143B THR* 2.8 50.8 + - + +
157B ARG* 3.4 50.8 - - - +
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Residues in contact with ASP 123 (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 ARG* 5.7 0.3 + - - -
121B TYR* 3.1 33.7 + - + +
122B ARG* 1.3 71.2 - - - +
124B LEU* 1.3 63.4 + - - +
125B ARG* 2.8 45.5 + - + +
126B LYS 4.6 0.3 + - - -
140B GLU* 5.7 2.9 - - - +
141B LEU 3.5 5.6 - - - +
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Residues in contact with LEU 124 (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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122B ARG* 3.6 3.1 + - + +
123B ASP* 1.3 76.1 + - - +
125B ARG* 1.3 72.4 + - - +
126B LYS* 3.3 9.2 + - + +
141B LEU* 3.1 29.0 + - + +
142B GLY* 3.6 26.0 - - - +
143B THR* 3.9 9.2 - - + -
159B ASN* 3.8 21.8 - - - +
194B LEU* 4.7 8.5 - - + -
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Residues in contact with ARG 125 (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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123B ASP* 2.8 37.1 + - - +
124B LEU* 1.3 81.5 - - - +
126B LYS* 1.3 58.4 + - - +
141B LEU 4.1 0.2 + - - -
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Residues in contact with LYS 126 (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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123B ASP* 4.6 0.8 + - - -
124B LEU* 3.3 11.8 - - + +
125B ARG* 1.3 80.2 - - - +
127B GLY* 1.3 67.0 + - - +
140B GLU* 3.7 3.0 - - - +
141B LEU* 2.7 53.3 + - + +
190B PRO* 3.5 32.6 - - - +
191B ASP* 4.4 6.9 + - - -
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Residues in contact with GLY 127 (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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126B LYS* 1.3 90.0 - - - +
128B VAL* 1.3 63.7 + - - +
138B GLU* 4.8 4.3 - - - -
139B GLY 3.2 11.2 - - - -
140B GLU* 4.3 4.9 - - - -
190B PRO* 5.8 0.7 - - - +
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Residues in contact with VAL 128 (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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98B ASN* 5.5 0.9 - - - +
127B GLY* 1.3 75.0 - - - +
129B TYR* 1.3 64.7 + - - +
130B VAL* 3.8 15.5 - - + -
137B TRP* 3.8 24.4 - - + -
138B GLU* 3.5 6.8 + - - +
139B GLY 2.8 42.3 + - - +
141B LEU* 3.7 32.1 - - + -
161B ALA* 4.5 0.7 - - + -
189B ARG* 4.0 5.8 - - + +
190B PRO* 3.8 34.1 - - + -
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Residues in contact with TYR 129 (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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307A LYS* 3.3 28.5 - - - +
128B VAL* 1.3 76.5 - - - +
130B VAL* 1.3 65.8 + - - +
131B PRO* 3.4 31.5 - - + +
136B LYS* 3.1 51.0 + - + +
137B TRP 3.8 8.3 - - - -
138B GLU* 3.7 20.4 + - + +
189B ARG* 4.5 5.7 - - - +
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Residues in contact with VAL 130 (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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98B ASN* 4.7 4.3 - - - +
128B VAL* 3.8 7.8 + - + -
129B TYR* 1.3 80.3 - - - +
131B PRO* 1.3 60.9 - - + +
132B TYR* 3.7 21.0 - - + +
136B LYS* 3.4 3.8 - - - -
137B TRP* 3.0 69.7 + - + -
189B ARG* 3.6 26.7 - - + -
456B Z76 3.4 31.9 - - + -
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Residues in contact with PRO 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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129B TYR* 3.4 45.3 - - + +
130B VAL* 1.3 88.0 - - + +
132B TYR* 1.3 64.3 + - - +
136B LYS* 3.5 12.6 - - + -
189B ARG* 5.4 8.9 + - + +
456B Z76 3.8 17.3 + - - +
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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