Contacts of the strand formed by residues 140 - 151 (chain A) in PDB entry 2PMW
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ALA* 3.7 29.9 + - + +
80A VAL* 4.3 9.0 - - + -
81A VAL 4.1 3.4 - - - +
82A LEU* 3.8 15.5 - - + -
83A LYS* 4.0 11.9 - - - -
94A THR* 4.8 0.7 - - + -
134A ALA 3.5 20.9 - - - +
135A LEU* 4.5 2.0 - - + +
137A LEU* 3.3 29.9 + - + +
138A PRO 3.2 4.0 - - - +
139A HIS* 1.3 78.5 - - - +
141A ASP* 1.3 62.4 + - - +
142A TYR 3.8 8.1 - - - +
143A ILE* 4.1 22.4 - - + -
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Residues in contact with ASP 141 (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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61A THR 4.8 0.5 - - - +
62A ALA* 3.3 20.8 - - - -
63A THR* 3.6 1.9 + - - -
81A VAL* 2.8 18.2 + - + +
82A LEU 3.8 15.6 - - - +
83A LYS* 3.9 17.5 - - - +
84A GLU* 5.1 2.9 + - - +
139A HIS 3.4 1.4 + - - -
140A VAL* 1.3 74.1 - - - +
142A TYR* 1.3 82.3 + - + +
295B ARG* 4.1 9.5 + - - -
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Residues in contact with TYR 142 (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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62A ALA* 4.4 0.2 - - - -
63A THR* 3.2 19.3 - - - +
65A HIS* 4.1 7.9 - + + -
81A VAL* 2.8 68.2 + - + +
119A LEU* 4.5 0.7 - - - +
140A VAL* 3.8 4.3 - - - +
141A ASP* 1.3 95.2 - - + +
143A ILE* 1.3 71.6 + - - +
144A GLU* 4.7 4.0 - - + -
295B ARG* 3.4 63.5 - - + +
296B VAL* 3.6 27.9 - - + +
299B ALA* 3.8 16.7 - - + +
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Residues in contact with ILE 143 (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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63A THR 3.0 6.3 + - - +
64A PHE* 3.4 10.0 - - + -
65A HIS* 2.9 25.6 + - - -
78A TYR* 4.0 17.7 - - + -
79A VAL 3.3 10.5 - - - +
80A VAL* 4.0 22.4 - - + -
126A MET* 5.6 0.4 - - + -
131A LEU* 3.7 24.2 - - + -
134A ALA* 3.6 36.8 - - + +
135A LEU* 3.5 29.6 - - + +
140A VAL* 4.1 3.1 - - + -
142A TYR* 1.3 81.5 - - - +
144A GLU* 1.3 63.7 + - - +
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Residues in contact with GLU 144 (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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65A HIS* 3.2 20.3 - - + +
66A ARG* 5.0 2.7 - - - -
78A TYR* 4.4 3.6 - - - -
79A VAL* 2.7 44.6 + - + +
142A TYR* 4.3 5.9 - - + -
143A ILE* 1.3 73.9 - - - +
145A GLU* 1.3 75.0 + - - +
146A ASP 3.5 0.2 + - - -
147A SER* 5.0 2.4 + - - -
261B VAL* 4.3 6.9 - - - +
294B SER* 2.5 28.5 + - - -
295B ARG* 3.1 16.8 + - - +
296B VAL* 3.0 45.5 + - + +
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Residues in contact with GLU 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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64A PHE* 4.0 6.1 - - + -
65A HIS 2.9 9.1 + - - +
66A ARG* 3.5 26.8 + - + +
67A CYS 4.6 1.9 + - - -
73A ARG* 2.7 58.8 + - - +
74A LEU 3.8 9.2 - - - +
75A PRO* 3.3 22.3 - - + +
77A THR 3.9 0.9 - - - +
78A TYR* 3.6 33.4 + - + -
144A GLU* 1.3 86.0 - - - +
146A ASP* 1.3 75.8 + - - +
147A SER* 3.8 4.2 + - - -
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Residues in contact with ASP 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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74A LEU* 3.0 34.4 + - + +
77A THR* 3.0 35.8 + - + +
78A TYR* 4.5 0.6 - - - +
79A VAL* 5.0 7.1 - - + +
123A LEU* 5.1 0.7 - - - -
144A GLU* 3.5 3.9 + - - -
145A GLU* 1.3 82.0 - - - +
147A SER* 1.3 66.9 + - - +
260B THR* 3.7 14.0 - - - +
261B VAL* 3.4 10.2 + - - +
262B SER* 2.6 51.4 + - - -
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Residues in contact with SER 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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67A CYS* 3.7 29.4 - - - +
72A TRP 3.2 16.2 - - - -
73A ARG* 4.3 0.2 - - - -
74A LEU* 3.6 10.1 - - - +
144A GLU* 5.0 3.5 + - - -
145A GLU 4.5 3.6 + - - -
146A ASP* 1.3 80.5 + - - +
148A SER* 1.3 63.9 + - - +
260B THR* 3.3 4.0 - - - -
261B VAL* 2.9 43.8 + - - +
292B GLY 5.4 3.6 + - - -
294B SER* 5.4 2.1 - - - -
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Residues in contact with SER 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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71A PRO 5.3 0.5 + - - -
72A TRP* 2.9 24.4 + - - +
74A LEU* 3.9 19.1 - - - +
147A SER* 1.3 79.0 + - - +
149A VAL* 1.3 66.4 + - - +
150A PHE* 3.6 31.0 - - - -
258B LYS* 4.2 15.5 + - - +
259B GLY 3.3 10.6 + - - -
261B VAL* 4.9 0.2 - - - +
291B GLY* 3.6 13.7 - - - -
292B GLY 4.6 1.7 + - - -
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Residues in contact with VAL 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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148A SER* 1.3 77.7 - - - +
150A PHE* 1.3 68.6 + - - +
252B VAL 5.2 0.2 - - - +
253B LEU* 4.3 9.9 - - + -
258B LYS* 3.6 2.3 - - - +
259B GLY* 2.8 52.2 + - - +
260B THR 3.7 4.0 - - - +
261B VAL* 4.1 24.9 - - + +
264B THR* 3.8 15.7 - - - +
289B LEU* 4.1 18.4 - - + -
290B ALA 3.3 10.5 - - - +
291B GLY* 4.0 13.9 - - - +
297B LEU* 4.7 8.3 - - + -
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Residues in contact with PHE 150 (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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72A TRP* 3.6 48.5 - + - -
148A SER* 3.6 31.9 - - - -
149A VAL* 1.3 78.2 - - - +
151A ALA* 1.3 68.0 + - - +
152A GLN* 2.8 24.0 + - - +
253B LEU* 4.5 0.9 - - - -
256B GLN 6.0 0.7 - - - -
257B GLY 3.6 4.7 - - - +
258B LYS* 3.5 32.1 - - + -
289B LEU* 3.3 6.0 - - - -
290B ALA 2.8 29.9 + - - -
318B PHE* 5.4 2.7 - + + -
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Residues in contact with ALA 151 (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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150A PHE* 1.3 73.9 - - - +
152A GLN* 1.3 69.8 + - - +
226B HIS* 3.6 32.5 - - + +
253B LEU* 3.8 14.5 - - + +
257B GLY* 2.9 26.9 + - - +
288B PRO 3.8 7.4 - - - -
317B ASN* 5.0 0.3 + - - -
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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