Contacts of the strand formed by residues 144 - 149 (chain A) in PDB entry 2P1E
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 VAL 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A SER 4.2 1.1 - - - +
75A THR* 3.0 22.1 + - - +
106A GLY* 3.7 19.1 - - - +
118A VAL* 4.6 1.3 - - + +
133A VAL* 4.0 15.5 - - + -
134A ILE 3.2 9.9 - - - +
135A ASP* 3.6 21.5 - - - +
136A ALA 4.2 0.9 - - - +
142A GLY 3.6 9.4 - - - +
143A HIS* 1.3 104.1 + - - +
145A LEU* 1.3 63.0 + - - +
146A TYR* 3.4 42.0 - - + +
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU 3.7 0.5 - - - +
133A VAL* 3.6 4.5 - - - -
134A ILE* 2.8 59.8 + - + +
136A ALA* 3.9 16.2 - - + -
144A VAL* 1.3 84.0 - - - +
146A TYR* 1.3 65.0 + - - +
147A LYS 4.1 0.2 - - - -
160A LEU* 4.2 13.9 - - + -
161A PHE 3.3 9.4 - - - +
162A THR* 3.8 30.5 - - + +
165A THR* 3.9 20.6 - - + +
185A ALA* 5.2 2.2 - - - +
188A LYS* 5.8 0.2 - - + -
189A VAL* 3.7 30.5 - - + -
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Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.8 3.4 - - + -
73A LEU* 3.7 24.0 - - + -
74A SER 2.8 37.5 + - - -
75A THR* 3.8 20.4 - - + -
104A VAL* 3.4 31.4 + - + +
105A GLY* 3.5 8.0 - - - -
118A VAL* 4.4 0.7 - - + -
131A VAL* 3.7 27.8 - - + -
132A GLU 3.5 1.8 - - - -
133A VAL* 4.1 15.9 - - + -
144A VAL* 3.4 20.6 - - + +
145A LEU* 1.3 77.0 - - - +
147A LYS* 1.3 58.9 + - - +
148A VAL* 3.9 2.0 - - + -
159A ALA 3.3 4.7 - - - +
160A LEU* 3.4 3.2 - - - -
161A PHE* 2.8 54.7 + - + -
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A SER* 3.6 2.3 + - - +
131A VAL* 3.5 0.9 - - - -
132A GLU* 2.8 74.7 + - + +
134A ILE* 4.5 12.8 - - + -
145A LEU 4.1 0.4 + - - -
146A TYR* 1.3 71.4 - - - +
148A VAL* 1.3 60.2 + - - +
149A GLN* 3.2 31.4 + - - +
158A VAL* 3.6 17.7 - - + -
159A ALA 3.6 3.4 - - - -
160A LEU* 4.0 14.6 - - + -
192A ILE* 3.6 33.7 - - + -
193A HIS* 4.2 13.3 - - - -
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.6 12.9 - - + -
29A ILE* 4.3 15.0 - - + -
126A VAL* 6.1 0.2 - - + -
129A LEU* 4.2 27.6 - - + -
130A SER 3.3 9.2 - - - +
131A VAL* 4.1 26.7 - - + -
146A TYR* 4.3 1.8 - - + +
147A LYS* 1.3 76.3 - - - +
149A GLN* 1.3 66.7 + - - +
158A VAL* 3.3 3.3 - - - -
159A ALA* 2.7 46.2 + - + +
161A PHE* 3.6 30.1 - - + -
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Residues in contact with GLN 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.9 8.5 - - - -
129A LEU* 3.4 9.9 - - - +
130A SER* 2.7 51.3 + - - +
132A GLU* 5.4 0.6 + - - -
147A LYS* 3.2 27.8 - - - +
148A VAL* 1.3 76.7 - - - +
150A HIS* 1.3 62.1 + - - +
151A PRO* 3.4 3.7 - - + +
154A PRO* 3.7 29.0 - - - +
157A GLY 3.4 12.8 - - - +
158A VAL* 3.7 20.1 - - + +
200A LEU* 4.7 5.4 - - - +
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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