Contacts of the strand formed by residues 125 - 130 (chain B) in PDB entry 1URP
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 LYS 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLY 4.8 3.4 - - - +
124B ALA* 1.3 71.6 - - - +
126B VAL* 1.3 58.4 + - - +
155B ASN* 3.4 31.0 - - + +
157B LEU* 4.1 15.7 - - + -
182B ASP* 2.7 48.9 + - + +
183B VAL* 4.7 0.2 - - - -
184B GLN* 2.7 49.6 + - - +
185B ALA 3.3 4.9 + - - -
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Residues in contact with VAL 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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116B ILE* 3.9 29.2 - - + -
124B ALA* 4.1 10.5 - - + +
125B LYS* 1.3 78.2 - - - +
127B ILE* 1.3 65.8 + - - +
145B PHE* 3.9 22.0 - - + -
154B PHE* 4.1 17.0 - - + -
155B ASN 2.8 16.7 + - - +
156B VAL* 3.3 23.4 - - + -
157B LEU* 2.7 31.9 + - - +
183B VAL* 4.3 0.7 - - - -
185B ALA* 3.2 15.9 - - + +
186B VAL* 5.4 0.2 - - - -
187B PHE 5.7 0.4 - - - +
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Residues in contact with ILE 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 VAL* 1.3 81.1 - - - +
128B GLU* 1.3 68.8 + - - +
129B LEU* 4.4 2.9 - - + -
145B PHE* 5.4 0.6 - - - -
157B LEU* 4.1 11.0 - - + -
158B ALA* 3.4 10.8 - - + +
173B MET* 3.9 27.8 - - + -
176B LEU* 3.8 41.3 - - + +
180B HIS* 4.2 15.0 - - + -
183B VAL* 3.6 34.3 - - + -
185B ALA 2.9 5.8 + - - +
186B VAL* 3.2 9.1 - - + +
187B PHE* 3.0 23.9 + - - +
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Residues in contact with GLU 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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127B ILE* 1.3 75.8 - - - +
129B LEU* 1.3 74.8 + - - +
130B GLN* 4.3 5.1 + - + -
142B GLY* 3.9 5.4 - - - -
145B PHE* 3.5 37.4 - - + +
146B GLN* 4.2 10.7 + - - -
156B VAL* 4.5 2.6 - - + +
158B ALA 3.0 8.3 + - - +
159B SER* 3.1 24.8 + - - +
160B GLN 3.1 25.3 + - - +
187B PHE* 3.3 27.8 - - + +
189B GLN* 3.1 24.8 + - - +
146D GLN* 5.0 0.5 - - - +
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Residues in contact with LEU 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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127B ILE* 4.4 3.8 - - + -
128B GLU* 1.3 75.8 - - - +
130B GLN* 1.3 61.0 - - - +
160B GLN 3.4 4.0 - - - +
162B ALA* 4.6 2.5 - - + -
169B GLY* 3.9 21.3 - - - +
172B VAL* 3.9 29.4 - - + -
173B MET* 4.4 8.5 - - + +
176B LEU* 4.0 16.6 - - + -
186B VAL* 4.3 10.5 - - + -
187B PHE 2.9 8.3 + - - -
188B ALA* 4.0 13.2 - - + -
189B GLN* 3.0 27.5 + - - +
193B MET* 3.5 20.4 - - + +
197B ALA* 3.7 29.4 - - + -
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Residues in contact with GLN 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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128B GLU* 4.3 5.5 + - + -
129B LEU* 1.3 74.4 - - - +
131B GLY* 1.3 65.4 + - - +
133B ALA* 6.1 1.2 - - - +
138B ALA* 5.2 2.9 - - + +
159B SER* 3.0 32.3 + - - +
160B GLN* 2.7 22.7 + - - +
161B PRO* 3.3 20.1 - - + +
162B ALA 2.8 29.7 + - - -
189B GLN* 3.5 21.3 - - - +
193B MET* 3.1 8.1 - - - +
146D GLN* 4.6 23.8 + - - +
150D ALA* 4.2 5.6 - - - +
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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