Contacts of the strand formed by residues 34 - 41 (chain B) in PDB entry 4PH8
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 ILE 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN* 3.8 23.1 - - - +
26B VAL* 4.0 25.6 - - + -
30B SER* 5.4 0.4 - - - +
32B THR 3.6 12.3 - - - +
33B PRO* 1.3 71.7 - - - +
35B GLY* 1.3 62.1 + - - +
36B PHE* 3.5 29.7 - - + -
113B SER* 3.3 3.8 - - - -
114B VAL* 2.7 47.8 + - + +
116B PRO* 4.0 12.1 - - + -
121B LEU* 3.7 31.0 - - + -
153B LEU* 4.2 13.7 - - + -
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Residues in contact with GLY 35 (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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21B THR* 4.2 5.1 - - - +
24B GLN* 3.0 27.9 + - - +
33B PRO 3.9 3.0 + - - -
34B ILE* 1.3 74.4 - - - +
36B PHE* 1.3 62.1 - - - -
112B VAL 3.6 7.4 - - - -
113B SER* 4.5 4.0 - - - -
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Residues in contact with PHE 36 (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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21B THR* 3.7 4.3 - - - -
24B GLN* 3.4 20.9 - - - -
34B ILE* 3.5 34.1 - - + -
35B GLY* 1.3 71.9 - - - -
37B SER* 1.3 62.8 + - - +
64B TRP* 4.3 1.5 - - - -
66B LEU* 4.1 23.1 - - + -
78B LEU* 4.9 0.7 - - + -
111B SER* 3.2 4.2 - - - -
112B VAL* 2.9 49.1 + - + +
114B VAL* 3.8 22.7 - - + -
128B MET* 3.6 24.9 - - + -
151B ILE* 3.5 29.2 - - + -
152B ARG 4.5 2.0 - - - -
153B LEU* 4.2 22.7 - - + -
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Residues in contact with SER 37 (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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20B THR* 3.2 7.2 - - - -
21B THR* 2.8 41.4 + - - -
36B PHE* 1.3 76.9 - - - +
38B ALA* 1.3 63.2 + - - +
64B TRP* 4.8 1.8 - - - -
109B ASN* 5.8 2.5 - - - -
110B ALA 3.3 12.8 - - - -
111B SER* 4.0 9.0 - - - +
151B ILE* 3.9 4.7 - - - +
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Residues in contact with ALA 38 (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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18B ILE* 4.5 2.7 - - + -
19B THR 3.3 9.4 - - - +
20B THR* 4.2 4.7 - - + -
37B SER* 1.3 77.2 - - - +
39B LYS* 1.3 65.9 + - - +
55B LEU* 3.9 23.4 - - + +
64B TRP* 4.1 2.0 - - + -
109B ASN* 3.6 2.5 - - - +
110B ALA 2.9 31.0 + - - +
130B LEU* 3.5 29.8 - - + -
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Residues in contact with LYS 39 (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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17B THR 3.7 2.1 + - - +
18B ILE* 3.2 5.4 - - - +
19B THR* 2.7 72.3 + - - +
38B ALA* 1.3 72.1 - - - +
40B VAL* 1.3 65.1 + - - +
41B THR* 5.9 1.2 - - - +
55B LEU* 5.2 0.2 - - - -
107B PHE* 3.6 37.6 - - + -
108B LEU 3.0 9.6 - - - +
109B ASN* 3.2 30.3 - - - +
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Residues in contact with VAL 40 (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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16B VAL* 3.9 26.0 - - + -
17B THR 3.4 9.2 - - - +
18B ILE* 4.5 2.5 - - + -
39B LYS* 1.3 82.8 - - - +
41B THR* 1.3 68.7 + - - +
53B VAL* 3.9 28.5 - - + +
54B TRP 4.0 9.0 - - - +
55B LEU* 3.7 34.8 - - + -
106B LYS 4.0 0.3 - - - +
107B PHE* 3.5 3.4 - - - -
108B LEU* 2.8 35.4 + - + +
132B ALA* 4.0 8.5 - - + -
133B ALA 4.4 0.4 - - - +
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Residues in contact with THR 41 (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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15B PRO 3.8 1.2 - - - +
16B VAL* 4.0 0.9 - - - -
17B THR* 3.0 52.0 + - + +
39B LYS* 5.9 1.3 - - - +
40B VAL* 1.3 76.7 - - - +
42B THR* 1.3 80.1 + - - +
47B ILE* 4.0 5.0 - - - +
53B VAL* 4.2 4.6 - - - +
101B LEU* 4.1 4.7 - - - -
106B LYS* 2.6 29.2 + - - +
107B PHE* 3.6 27.8 - - + -
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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