Contacts of the strand formed by residues 28 - 36 (chain H) in PDB entry 1PPB
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 PRO 28 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25H GLY* 3.2 23.6 - - - +
26H MET 3.6 3.6 - - - +
27H SER* 1.3 82.1 - - - +
29H TRP* 1.3 74.9 + - + +
30H GLN 3.5 3.6 + - - +
46H LEU* 4.9 1.2 - - - +
68H ILE* 5.0 2.1 - - - +
69H GLY 5.1 0.5 + - - -
116H ASP 3.9 5.6 - - - +
117H TYR 3.3 34.7 - - - +
118H ILE* 3.4 5.2 - - - +
119H HIS* 3.0 42.7 + - + +
4L ARG* 3.7 21.1 - - + -
5L PRO* 4.6 1.1 - - + -
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Residues in contact with TRP 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H MET 4.2 11.7 - - - -
27H SER* 3.3 25.2 + - - -
28H PRO* 1.3 91.5 - - + +
30H GLN* 1.3 63.5 + - - +
31H VAL* 3.4 2.6 - - - +
45H SER* 3.3 4.3 - - - -
46H LEU* 2.8 48.5 + - - +
68H ILE* 5.9 0.2 - - - -
119H HIS* 3.2 21.6 + + - +
120H PRO 3.9 1.8 - - - -
121H VAL* 3.6 28.7 - - + -
137H ARG* 6.3 0.4 - - - -
198H PRO* 3.9 20.0 - - + +
200H VAL* 3.7 20.2 - - + +
207H TRP* 3.5 45.1 - + + -
2L GLY* 4.2 21.3 - - - -
4L ARG* 3.8 15.9 - - + -
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Residues in contact with GLN 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H SER* 3.0 24.1 + - - +
28H PRO 4.5 1.7 - - - +
29H TRP* 1.3 82.8 - - - +
31H VAL* 1.3 74.6 + - - +
43H GLY* 4.1 13.7 - - - -
44H ALA 3.8 7.6 + - - -
67H ARG 4.6 0.3 - - - +
68H ILE* 4.3 1.9 - - - +
69H GLY 4.1 17.0 + - - -
70H LYS 5.3 4.2 + - - +
139H THR* 2.7 42.0 + - - -
140H GLY* 3.9 9.9 - - - -
141H TRP* 3.5 30.1 - - + -
155H LEU* 3.8 15.7 - - + -
197H GLY* 4.3 4.0 - - - -
198H PRO* 3.5 9.8 - - - +
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Residues in contact with VAL 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H TRP 3.4 16.4 - - - +
30H GLN* 1.3 77.8 + - - +
32H MET* 1.3 62.5 + - - +
43H GLY* 3.4 6.1 - - - -
44H ALA* 2.9 49.2 + - + +
45H SER 4.0 1.8 - - - -
46H LEU* 3.7 18.2 - - + +
52H VAL* 3.9 8.7 - - + -
66H VAL* 3.6 34.8 - - + -
67H ARG 3.8 5.6 - - - +
68H ILE* 4.1 19.7 - - + -
141H TRP* 3.9 7.1 - - - -
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Residues in contact with MET 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H VAL* 1.3 74.7 - - - +
33H LEU* 1.3 60.2 + - - +
34H PHE* 3.3 33.7 + - + +
40H LEU* 3.5 34.3 - - + -
42H CYS 4.0 2.7 - - - +
66H VAL* 3.5 5.0 - - - -
67H ARG* 2.9 44.4 + - + +
70H LYS* 3.8 27.4 - - + -
72H SER 4.1 0.9 - - - +
73H ARG* 3.7 16.8 - - - +
141H TRP* 3.7 34.1 - - + -
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Residues in contact with LEU 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H VAL* 4.0 1.8 + - - +
32H MET* 1.3 72.3 - - - +
34H PHE* 1.3 55.4 + - - +
40H LEU* 3.7 2.8 - - - -
41H LEU* 2.9 47.6 + - + -
42H CYS* 2.9 32.6 + - + +
43H GLY* 4.5 4.2 - - - +
44H ALA* 4.9 4.9 - - + -
54H THR* 4.1 19.1 - - + +
58H CYS* 4.3 2.9 - - + -
59H LEU* 4.0 16.8 - - + -
64H LEU* 4.2 17.3 - - + -
65H LEU 3.8 13.2 - - - +
66H VAL* 4.0 10.8 - - + -
106H MET* 3.8 30.7 - - + -
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Residues in contact with PHE 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H MET* 3.3 32.5 - - + +
33H LEU* 1.3 74.6 - - - +
35H ARG* 1.3 66.7 + - - +
38H GLN* 3.8 21.1 - - + -
39H GLU* 3.5 31.0 - - - -
40H LEU* 3.7 17.3 - - + -
41H LEU* 4.6 0.2 - - - +
64H LEU* 3.3 7.0 - - - +
65H LEU* 2.8 59.9 + - + +
67H ARG* 3.8 35.0 - - - -
73H ARG 5.1 4.3 - - - -
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Residues in contact with ARG 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H PHE* 1.3 82.4 - - - +
36H LYS* 1.3 82.7 + - - +
37H PRO* 3.3 33.6 - - - +
38H GLN* 3.5 14.4 - - - +
39H GLU* 2.8 45.4 + - + +
41H LEU* 3.4 24.8 - - + +
60H PHE* 3.9 30.2 + - - +
63H ASP* 3.7 10.5 - - + +
64H LEU* 4.4 1.1 - - + -
65H LEU* 5.1 0.4 - - - +
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Residues in contact with LYS 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ARG* 1.3 72.6 - - - +
36H SER* 1.3 66.3 + - + +
37H PRO 3.9 0.4 - - - -
38H GLN* 3.3 28.4 - - - +
62H ASN* 3.3 42.5 + - - +
63H ASP* 2.9 22.2 + - - +
64H LEU 3.9 5.8 + - - +
65H LEU* 4.1 31.2 - - + -
84H MET* 4.5 21.4 - - - +
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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