Contacts of the strand formed by residues 38 - 48 (chain E) in PDB entry 3PB1
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 38 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E TYR* 3.8 33.1 - - + -
35E ARG 3.4 5.2 - - - +
36E ARG* 3.8 34.3 - - + +
37E SER* 1.3 86.2 - - + +
39E THR* 1.3 65.7 + - - +
65E ILE* 4.4 13.2 - - + -
67E TYR* 6.5 0.2 - - + -
74E ASN* 5.7 0.9 - - - +
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Residues in contact with THR 39 (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 TYR* 3.2 8.0 - - - -
35E ARG 2.8 36.7 + - - -
37E HIS* 3.0 41.7 - - + +
38E VAL* 1.3 78.2 - - - +
40E TYR* 1.3 67.4 + - - +
41E VAL* 4.0 5.5 - - - +
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Residues in contact with TYR 40 (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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30E PHE* 3.5 16.1 - - - -
32E ALA* 3.7 12.7 - - + -
33E ILE 3.6 16.6 - - - -
34E TYR* 3.6 31.1 - + + -
39E THR* 1.3 78.3 + - - +
41E VAL* 1.3 62.2 + - - +
42E CYS 3.1 36.2 + - - -
43E GLY* 3.2 10.2 + - - -
73E LEU* 3.6 26.9 - - + -
141E PHE* 3.7 23.8 + + + +
151E TYR* 5.7 8.8 - + + -
193E GLY* 3.5 25.5 + - - -
348I ALA* 3.3 22.2 - - + +
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Residues in contact with VAL 41 (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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33E ILE* 2.9 16.8 + - + +
34E TYR 4.4 0.4 - - - -
35E ARG* 3.6 39.0 - - + +
39E THR* 4.0 6.1 - - - +
40E TYR* 1.3 84.2 - - - +
42E CYS* 1.3 76.4 + - + +
58E CYS* 3.5 26.5 - - + +
59E PHE* 5.1 2.0 - - + -
64E TYR* 4.7 8.5 - - + -
193E GLY* 4.5 1.2 - - - -
347I MET* 3.9 15.0 - - + -
348I ALA* 3.0 32.2 + - - +
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Residues in contact with CYS 42 (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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33E ILE* 2.9 36.2 + - + +
40E TYR* 3.1 16.3 + - - -
41E VAL* 1.3 90.5 - - + +
43E GLY* 1.3 65.9 - - - +
54E SER* 4.4 1.6 - - - +
58E CYS* 2.0 54.1 - - + -
59E PHE* 4.9 1.1 - - + -
193E GLY 4.5 2.2 - - - -
195E ALA* 3.2 11.0 - - - +
347I MET* 3.5 17.0 - - - -
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Residues in contact with GLY 43 (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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30E PHE* 3.8 9.9 - - - -
31E ALA 3.4 8.3 - - - -
33E ILE* 3.3 5.7 - - - +
40E TYR* 3.2 14.6 + - - -
42E CYS* 1.3 75.6 - - - +
44E GLY* 1.3 57.9 + - - -
54E SER* 2.9 21.7 + - - -
193E GLY 4.4 3.0 + - - -
194E ASP* 4.7 1.7 + - - -
195E ALA 2.8 11.5 + - - -
196E GLY* 3.4 9.8 - - - -
197E GLY* 4.0 5.8 - - - -
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Residues in contact with GLY 44 (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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30E PHE* 3.7 10.9 - - - -
31E ALA* 2.9 30.3 + - - -
33E ILE* 4.1 2.2 - - - -
43E GLY* 1.3 74.7 - - - -
45E SER* 1.3 66.6 + - - -
52E VAL* 3.9 11.0 - - - -
53E ILE 3.4 12.3 - - - -
54E SER* 4.3 0.2 - - - -
196E GLY 3.4 6.8 + - - -
197E GLY* 4.0 1.6 - - - -
198E PRO* 4.4 0.5 - - - +
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Residues in contact with SER 45 (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 TRP* 3.5 8.5 - - - -
31E ALA* 5.0 0.2 - - - -
44E GLY* 1.3 77.5 + - - -
46E LEU* 1.3 63.0 + - - +
47E ILE 3.4 1.0 + - - -
52E VAL* 3.4 6.2 - - - +
53E ILE* 2.8 51.7 + - - +
121E ILE* 4.2 18.8 - - - -
196E GLY 4.6 0.5 + - - -
197E GLY 4.4 1.0 - - - -
198E PRO* 3.3 31.2 - - - +
209E LEU* 3.8 6.5 - - - +
212E ILE* 6.1 0.2 - - - +
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Residues in contact with LEU 46 (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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28E PRO 5.5 0.4 - - - +
29E TRP* 2.9 18.5 + - - +
31E ALA* 5.0 0.4 - - - +
45E SER* 1.3 69.8 - - - +
47E ILE* 1.3 57.5 + - - +
48E SER 3.1 24.7 - - - +
49E PRO* 4.1 9.0 - - + +
51E TRP 3.4 11.0 - - - +
52E VAL* 4.0 16.7 - - + +
68E LEU* 3.9 24.7 - - + -
108E ILE* 4.3 2.2 - - + -
112E ALA* 3.8 21.1 - - + -
118E ILE* 4.1 9.6 - - + -
119E GLN 3.8 19.7 - - - +
120E THR* 3.4 14.7 - - + -
121E ILE* 3.0 29.1 + - - +
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Residues in contact with ILE 47 (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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45E SER 3.4 1.5 + - - +
46E LEU* 1.3 76.0 - - - +
48E SER* 1.3 64.7 + - - +
51E TRP* 3.0 24.7 + - + +
53E ILE* 3.7 29.4 - - + -
105E LEU* 4.0 25.4 - - + -
120E THR* 3.7 12.6 - - - +
121E ILE* 4.1 19.5 - - + +
123E LEU* 3.9 33.2 - - + +
209E LEU* 4.5 0.2 - - + -
238E ILE* 4.0 21.1 - - + -
242E THR* 4.2 10.3 - - + -
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Residues in contact with SER 48 (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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1E SO4 2.5 30.6 + - - -
46E LEU* 3.1 17.5 - - - +
47E ILE* 1.3 81.8 - - - +
49E PRO* 1.4 78.1 - - - +
50E CYS 3.1 1.4 + - - -
51E TRP* 3.2 22.3 + - - +
120E THR* 3.6 10.2 - - - +
242E THR* 5.4 0.9 - - - +
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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