Contacts of the strand formed by residues 27 - 37 (chain B) in PDB entry 3PII
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 GLU 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B THR 4.5 0.2 - - - +
23B ILE* 4.1 8.1 - - + -
24B SER* 3.1 41.8 + - - +
25B TYR 3.1 16.1 - - - +
26B GLY* 1.3 81.2 - - - +
28B VAL* 1.3 65.4 + - - +
71B GLY* 2.9 26.2 + - - -
74B VAL* 3.6 1.4 - - - +
89B TYR* 4.2 9.4 + - - -
125B ARG* 3.2 32.7 + - + +
126B ALA 3.2 12.1 - - - +
127B ALA* 5.4 3.3 - - - +
128B ALA* 4.3 0.7 - - - -
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Residues in contact with VAL 28 (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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23B ILE* 3.9 7.6 - - - +
27B GLU* 1.3 79.5 - - - +
29B LEU* 1.3 59.9 + - - +
30B VAL* 3.9 19.9 + - + -
67B VAL* 4.3 16.2 - - + -
69B GLU 3.5 13.5 - - - +
70B VAL* 4.0 11.4 - - + -
74B VAL* 4.3 6.1 - - + -
77B LEU* 3.9 17.3 - - + -
124B CYS 3.7 0.3 - - - +
125B ARG* 3.5 4.7 - - - -
126B ALA* 2.8 37.7 + - + +
128B ALA* 3.9 17.0 - - + -
131B VAL* 4.1 18.2 - - + -
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Residues in contact with LEU 29 (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 LYS* 3.9 28.9 - - - +
21B PRO* 4.1 24.9 - - + +
23B ILE* 3.9 13.4 - - + +
28B VAL* 1.3 71.4 - - - +
30B VAL* 1.3 56.3 + - - +
67B VAL* 3.7 2.4 - - - -
68B GLU* 2.8 40.5 + - + +
69B GLU* 3.0 44.5 + - + +
123B TYR* 4.0 27.8 - - + -
124B CYS 3.7 16.6 - - - +
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Residues in contact with VAL 30 (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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28B VAL* 4.1 17.7 - - + -
29B LEU* 1.3 76.0 - - - +
31B ARG* 1.3 68.0 + - - +
32B ILE* 3.6 22.8 + - + -
64B VAL* 4.8 0.4 - - - -
65B GLY* 4.1 16.4 - - - +
66B ILE 3.5 6.3 - - - +
67B VAL* 4.3 6.5 - - + -
83B VAL* 3.9 26.0 - - + +
85B ILE* 4.2 18.2 - - + -
123B TYR* 3.2 9.1 - - - -
124B CYS 2.8 39.0 + - - +
126B ALA* 4.7 2.2 - - + -
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Residues in contact with ARG 31 (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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29B LEU 4.0 1.2 + - - -
30B VAL* 1.3 70.5 - - - +
32B ILE* 1.3 68.7 + - - +
33B LYS* 3.3 18.2 + - + +
65B GLY* 3.1 1.2 - - - -
66B ILE* 2.7 59.3 + - - +
68B GLU* 2.8 33.2 + - + +
122B GLU* 3.5 11.9 - - + +
123B TYR* 3.6 23.7 + - + -
337B GLU* 3.7 24.1 + - - +
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Residues in contact with ILE 32 (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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30B VAL* 3.6 20.2 + - + -
31B ARG* 1.3 74.4 - - - +
33B LYS* 1.3 62.5 + - - +
34B ALA 3.7 23.6 - - - +
35B CYS* 4.5 0.4 - - + -
63B GLY 4.2 11.7 - - - -
64B VAL 3.6 7.4 - - - +
65B GLY* 4.2 0.2 - - - -
85B ILE* 4.2 8.3 - - + -
119B GLY* 3.6 28.3 - - - +
121B ALA 3.1 22.7 - - - +
122B GLU* 3.0 12.5 + - - +
123B TYR 4.3 2.9 - - - -
124B CYS* 4.0 25.8 - - + -
336B LEU* 3.8 23.6 - - + +
337B GLU* 5.2 2.9 - - - +
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Residues in contact with LYS 33 (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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31B ARG* 3.3 18.6 + - + +
32B ILE* 1.3 75.7 - - - +
34B ALA* 1.3 61.8 + - - +
64B VAL 2.9 4.8 + - - -
65B GLY* 3.9 5.8 - - - -
66B ILE* 3.9 30.7 - - + -
140B PHE* 3.7 35.2 - - + -
335B THR* 4.0 6.9 + - - -
336B LEU* 3.7 17.3 + - - +
337B GLU* 3.3 44.4 + - + +
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Residues in contact with ALA 34 (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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32B ILE* 3.7 6.7 - - - +
33B LYS* 1.3 81.6 - - - +
35B CYS* 1.3 60.9 + - - +
63B GLY* 3.6 1.2 - - - -
64B VAL* 2.9 35.7 + - + +
140B PHE* 4.4 21.5 - - + +
141B GLU* 4.7 8.1 - - + +
144B ALA* 5.0 0.2 - - - -
333B VAL* 3.9 15.9 - - + -
334B LEU 3.2 14.6 - - - +
335B THR* 4.7 3.6 - - - +
336B LEU* 4.7 0.7 - - - -
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Residues in contact with CYS 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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32B ILE* 4.4 0.9 - - + +
34B ALA* 1.3 75.0 - - - +
36B GLY* 1.3 73.8 + - - +
60B GLY* 3.6 13.5 - - - -
62B GLU 3.5 4.0 - - - -
63B GLY* 3.6 19.1 - - - -
119B GLY* 3.3 29.4 - - - +
120B TYR* 3.6 21.5 - - + -
333B VAL* 3.9 3.1 - - - -
334B LEU* 2.7 46.0 + - + +
336B LEU* 4.5 2.0 - - + +
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Residues in contact with GLY 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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35B CYS* 1.3 88.7 - - - +
37B VAL* 1.3 61.3 + - - +
41B ASP* 3.6 9.2 - - - +
60B GLY* 4.8 0.2 - - - -
62B GLU* 3.0 42.2 + - - +
120B TYR* 3.9 0.2 - - - -
144B ALA* 3.9 8.8 - - - +
145B PRO* 5.9 0.2 - - - -
332B VAL 4.0 6.3 - - - -
333B VAL* 4.3 6.5 - - - -
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Residues in contact with VAL 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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36B GLY* 1.3 75.5 - - - +
38B CYS* 1.3 66.3 + - - +
41B ASP* 3.5 3.6 - - - +
62B GLU* 3.9 3.5 + - - -
120B TYR* 3.3 21.8 - - + +
316B ILE* 4.3 3.1 - - + -
319B VAL* 4.5 6.5 - - + -
320B PHE* 3.7 17.9 - - + -
323B MET* 3.6 24.9 - - + +
331B ARG* 3.6 21.7 + - - +
332B VAL* 3.1 26.9 + - + +
334B LEU* 3.7 34.3 - - + -
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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