Contacts of the strand formed by residues 151 - 157 (chain E) in PDB entry 3PHW
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 HIS 151 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D GLN* 3.8 11.0 + - - -
37D PRO* 3.7 19.3 - - + -
38D PRO* 4.3 10.3 - - + +
39D ASP* 2.8 23.5 + - - -
34E GLN 4.1 14.3 + - - -
35E PRO 4.2 4.7 - - - -
36E GLY* 4.3 1.1 - - - -
40E CYS* 3.9 11.9 - - + -
145E LEU 3.4 0.5 - - - +
146E HIS* 3.3 9.2 + - - -
147E SER* 2.9 36.5 + - - +
149E GLN 3.9 0.4 - - - -
150E THR* 1.3 80.8 - - - +
152E PHE* 1.3 80.9 + - - +
153E ASP* 2.7 41.1 + - - -
75F GLY* 3.8 2.2 - - - -
76F NEH 3.8 10.0 - - - +
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Residues in contact with PHE 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLN* 3.9 1.7 - - - +
40E CYS* 3.3 16.3 - - - +
41E PHE* 3.8 33.4 - + + -
44E SER* 3.4 17.8 + - - +
100E GLY 3.6 12.1 - - - -
101E SER* 4.4 2.2 - - - -
118E ILE* 4.0 30.7 - - + -
144E LEU* 4.1 17.5 - - + -
145E LEU 3.2 12.3 - - - -
146E HIS* 3.6 21.8 - + + -
151E HIS* 1.3 92.2 + - - +
153E ASP* 1.3 61.4 + - - +
73F LEU* 3.9 17.0 - - + -
74F ARG 3.8 0.4 - - - -
75F GLY* 3.4 39.3 - - - -
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Residues in contact with ASP 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLN* 3.4 0.9 + - - -
31E ILE* 4.1 13.9 - - + -
32E VAL 3.8 7.4 - - - +
33E ARG* 2.9 36.4 + - - -
34E GLN* 2.9 24.7 + - - +
44E SER* 3.3 12.7 + - - -
144E LEU* 3.6 5.7 - - - +
145E LEU* 2.9 38.2 + - + +
147E SER* 4.4 3.3 + - - -
151E HIS* 2.7 35.3 + - - -
152E PHE* 1.3 70.2 - - - +
154E ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ILE* 3.6 5.2 - - - +
32E VAL* 2.8 37.2 + - + +
34E GLN* 3.9 17.9 - - - +
44E SER* 3.7 24.7 + - - +
47E GLU* 3.9 12.8 - - + -
48E LEU* 3.9 12.1 - - + -
143E ASN 4.0 3.4 - - - -
144E LEU* 4.7 0.2 - - - -
153E ASP* 1.3 76.0 - - - +
155E LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 155 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E ILE* 3.8 35.0 - - + -
29E PHE* 3.7 25.4 - - + -
30E GLU 3.4 1.6 - - - +
31E ILE* 3.8 20.2 - - + -
32E VAL* 5.3 0.4 - - - -
48E LEU* 3.5 12.2 - - - +
119E TRP* 3.5 32.3 - - + -
143E ASN* 3.0 26.7 + - + +
144E LEU 3.7 12.1 - - - +
145E LEU* 3.9 20.2 - - + +
154E ALA* 1.3 77.7 - - - +
156E ARG* 1.3 68.4 + - - +
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Residues in contact with ARG 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE* 3.3 3.1 - - - -
30E GLU* 2.7 64.8 + - - +
32E VAL* 3.7 21.9 - - + +
47E GLU* 2.9 45.8 + - - -
48E LEU* 3.7 15.3 - - + +
143E ASN* 6.1 0.4 - - - +
155E LEU* 1.3 77.9 - - - +
157E ILE* 1.3 66.7 + - - +
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Residues in contact with ILE 157 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E LEU* 4.0 10.8 - - + -
28E TYR 3.7 6.5 - - - +
29E PHE* 3.6 23.4 - - + -
30E GLU* 5.4 1.0 - - - +
138E VAL* 3.4 30.1 - - + +
139E PHE* 3.8 31.0 - - + +
143E ASN* 4.6 3.8 - - - +
156E ARG* 1.3 78.8 - - - +
158E LEU* 1.3 76.7 + - - +
159E PRO* 3.7 2.8 - - - +
161E PHE* 4.0 24.2 - - + +
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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