Contacts of the strand formed by residues 33 - 39 (chain A) in PDB entry 1PRX
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 TRP 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.8 1.8 - - - +
32A SER* 1.3 79.6 - - - +
34A GLY* 1.3 59.3 + - - +
65A ASN* 2.8 25.3 + - - +
66A VAL* 3.6 15.7 - - + -
67A LYS* 2.9 24.6 + - - +
136A VAL* 4.3 10.8 - - + -
137A PHE 3.3 20.4 - - - +
138A GLY* 3.6 7.4 - - - -
139A PRO* 3.6 25.9 - - + +
144A LYS* 3.7 33.9 - - + -
164A VAL* 6.0 2.7 - - + -
167A LEU* 4.0 37.0 - - + -
168A GLN* 3.4 38.1 - - + +
171A ALA* 4.2 19.7 - - + -
172A GLU* 5.8 1.2 + - - -
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Residues in contact with GLY 34 (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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25A PHE* 6.3 0.2 - - - -
29A LEU* 3.9 22.3 - - - +
32A SER 4.0 0.2 + - - -
33A TRP* 1.3 76.7 - - - +
35A ILE* 1.3 65.1 + - - +
36A LEU 4.2 0.2 - - - -
67A LYS 3.3 9.0 - - - -
69A ILE* 5.8 0.4 - - - -
135A PHE 3.6 0.7 - - - +
136A VAL* 3.4 3.1 - - - +
137A PHE* 2.7 46.0 + - - +
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Residues in contact with ILE 35 (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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25A PHE* 6.4 0.2 - - - -
34A GLY* 1.3 76.3 - - - +
36A LEU* 1.3 60.7 + - - +
37A PHE* 3.8 20.7 + - + -
61A PHE* 3.7 24.7 - - + -
66A VAL* 3.7 25.4 - - + -
67A LYS 3.1 5.7 + - - -
68A LEU* 3.9 9.1 - - + -
69A ILE* 3.1 31.7 + - - +
134A VAL* 3.5 29.2 - - + -
135A PHE 3.1 5.8 - - - +
136A VAL* 4.1 18.2 - - + -
160A ILE* 4.2 10.1 - - + -
164A VAL* 3.9 11.9 - - + -
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Residues in contact with LEU 36 (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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14A PHE* 4.7 7.9 - - + -
25A PHE* 4.0 24.2 - - + -
34A GLY 4.2 0.4 - - - -
35A ILE* 1.3 73.2 - - - +
37A PHE* 1.3 62.2 + - - +
38A SER* 3.8 18.6 - - - +
69A ILE* 3.3 17.9 - - + +
70A ALA 4.9 0.4 - - - -
71A LEU* 3.9 27.8 - - + +
103A ILE* 5.1 4.3 - - + -
114A LEU* 4.0 22.7 - - + -
133A VAL 3.5 3.3 - - - +
134A VAL* 3.2 6.2 - - - -
135A PHE* 2.7 53.6 + - + +
137A PHE* 4.2 9.8 - - + -
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Residues in contact with PHE 37 (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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35A ILE* 3.8 29.8 - - + -
36A LEU* 1.3 72.3 - - - +
38A SER* 1.3 60.2 + - - +
39A HIS* 3.6 11.8 - - + +
51A LEU* 4.8 4.7 - - + -
54A ALA* 4.5 11.0 - - + -
61A PHE* 5.6 0.9 - + - -
68A LEU* 3.6 34.1 - - + -
69A ILE 3.0 22.1 + - - +
70A ALA* 3.4 8.0 - - + -
71A LEU 2.9 27.5 + - - +
100A PHE* 5.7 2.9 - + - -
133A VAL 4.2 0.7 - - - -
134A VAL* 3.9 17.0 - - + +
155A ARG* 3.7 24.0 - - - +
157A PHE* 3.7 36.3 - + - -
160A ILE* 4.2 9.4 - - + -
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Residues in contact with SER 38 (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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36A LEU* 3.8 11.3 - - - +
37A PHE* 1.3 72.3 - - - +
39A HIS* 1.3 65.6 + - - +
71A LEU* 3.5 8.2 - - - +
116A MET* 3.2 30.6 - - - +
131A ALA 3.6 12.4 - - - +
132A ARG* 3.8 3.5 - - - -
133A VAL 2.8 35.0 + - - -
135A PHE* 4.2 1.2 - - - -
155A ARG* 2.9 23.1 + - - +
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Residues in contact with HIS 39 (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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37A PHE* 3.6 13.4 - - - +
38A SER* 1.3 76.7 + - - +
40A PRO* 1.3 71.6 - - + +
41A ARG 3.3 1.6 - - - +
47A CSO 3.0 37.9 - - + +
50A GLU* 3.1 26.2 - - + -
51A LEU* 3.1 39.2 - - + +
70A ALA* 4.6 3.6 - - + -
71A LEU* 2.9 14.4 + - - +
72A SER* 3.4 29.5 - - - +
73A ILE* 3.4 7.8 + - - +
82A TRP* 4.5 5.8 - + + -
102A ILE* 6.5 0.2 - - + -
131A ALA* 3.5 5.3 - - - +
132A ARG* 3.8 0.2 + - - -
155A ARG* 3.4 18.1 + - - -
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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