Contacts of the strand formed by residues 30 - 39 (chain B) in PDB entry 4O28
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 THR 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ALA* 6.1 0.2 - - + -
26B TYR* 4.5 11.4 - - + -
27B PRO* 2.6 32.4 + - + +
28B PRO 3.3 0.2 - - - -
29B ASN* 1.3 77.8 - - - +
31B SER* 1.3 59.5 + - - +
32B LYS 3.6 17.9 - - - +
33B VAL* 4.0 15.9 - - + -
139B PRO 4.0 1.4 - - - +
142B TYR* 3.3 33.5 - - + +
404B VAL* 4.6 4.7 - - + -
405B VAL 3.3 12.8 - - - +
406B THR* 3.0 18.4 + - - +
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Residues in contact with SER 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 ASN 3.6 4.9 + - - -
30B THR* 1.3 73.3 - - - +
32B LYS* 1.3 62.6 + - - +
136B ASN* 2.8 22.2 + - - -
139B PRO* 3.3 35.1 - - - +
142B TYR* 4.1 3.4 - - - -
405B VAL* 2.8 28.4 + - - +
408B GLY* 5.1 2.8 + - - -
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Residues in contact with LYS 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 THR* 3.6 2.8 - - - +
31B SER* 1.3 83.8 + - - +
33B VAL* 1.3 70.6 + - - +
34B TYR* 4.4 8.5 - - + +
135B GLU* 2.8 40.3 + - + +
136B ASN* 3.4 22.8 + - - +
137B THR* 5.7 0.8 - - - +
142B TYR* 4.8 0.2 - - - -
403B TYR* 4.6 11.2 - - + -
404B VAL* 3.2 10.2 - - - +
405B VAL* 3.1 48.9 + - + +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 4.1 28.7 - - + +
30B THR* 4.0 16.4 - - + -
32B LYS* 1.3 80.1 - - - +
34B TYR* 1.3 62.2 + - - +
35B SER* 4.1 0.4 - - - +
135B GLU* 3.4 6.6 - - - +
136B ASN* 2.9 11.3 + - - +
142B TYR* 3.2 25.8 - - + +
145B THR* 2.7 42.5 + - + +
146B ASN* 4.0 11.7 - - - +
401B CYS* 4.0 17.5 - - - -
403B TYR 3.9 3.1 - - - -
404B VAL* 4.3 5.2 - - + -
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Residues in contact with TYR 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 LYS* 4.5 3.1 - - + -
33B VAL* 1.3 74.2 - - - +
35B SER* 1.3 69.8 + - - +
117B LYS* 6.4 0.9 - - + -
133B THR* 3.3 32.3 + - + +
134B VAL 3.4 6.7 - - - -
135B GLU* 3.9 35.2 - - + -
401B CYS* 3.6 1.7 - - - -
402B SER* 3.0 42.6 + - - -
403B TYR* 2.9 38.9 + + + +
428B GLY 3.9 10.1 - - - -
429B ARG* 3.9 16.3 - - + +
430B LEU* 3.0 35.3 + - + -
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Residues in contact with SER 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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33B VAL* 4.1 1.2 - - - +
34B TYR* 1.3 77.8 - - - +
36B TYR* 1.3 63.9 + - - +
133B THR* 3.3 6.2 - - - -
134B VAL 2.8 30.8 + - - -
145B THR* 3.7 6.6 - - - +
146B ASN* 2.8 20.3 + - - -
399B PHE* 3.4 30.1 - - - -
400B LYS 3.1 12.3 - - - -
401B CYS* 3.3 16.6 + - - +
402B SER 4.3 0.9 - - - +
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Residues in contact with TYR 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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34B TYR* 5.2 0.4 - - + -
35B SER* 1.3 77.2 - - - +
37B PHE* 1.3 68.6 + - - +
38B GLU* 2.8 46.1 + - + -
130B VAL* 4.1 5.2 - - + -
132B PHE* 3.3 13.0 - - - +
133B THR* 4.0 7.6 - - + +
398B SER 3.6 1.2 - - - +
399B PHE* 3.2 9.5 - - - -
400B LYS* 2.9 60.7 + - + +
402B SER* 4.0 16.8 - - - +
425B SER* 3.6 7.1 - - - -
426B LYS* 2.8 45.3 + - + +
430B LEU* 3.4 27.4 - - + -
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Residues in contact with PHE 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 TYR* 1.3 75.4 - - - +
38B GLU* 1.3 67.4 + - - +
39B CYS* 4.5 1.3 - - - -
130B VAL* 3.9 2.3 - - - -
131B LEU* 2.9 43.4 + - + +
132B PHE* 2.9 54.2 + + + +
153B VAL* 4.2 26.0 - - + -
155B SER* 3.7 17.5 - - - -
156B TRP 4.4 2.9 - - - -
159B ILE* 3.5 26.5 - - + -
397B CYS* 3.5 32.8 - - + -
398B SER 3.2 19.7 - - - -
399B PHE* 4.5 2.7 - - + -
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Residues in contact with GLU 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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36B TYR* 2.8 38.3 + - + -
37B PHE* 1.3 80.0 - - - +
39B CYS* 1.3 61.7 + - - +
40B ARG* 3.7 34.0 - - + +
41B GLU 4.6 0.2 + - - -
128B GLY* 3.6 15.8 - - - -
129B ASN 3.4 22.0 - - - +
131B LEU* 4.4 1.3 - - - -
396B ASN 3.5 0.7 - - - +
397B CYS* 3.4 1.9 - - - -
398B SER* 2.9 38.7 + - - +
400B LYS* 5.8 1.1 - - + +
424B ARG 4.7 4.2 - - - +
425B SER* 4.7 0.7 - - - -
426B LYS* 3.5 20.3 + - - +
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Residues in contact with CYS 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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37B PHE* 4.5 2.5 - - - -
38B GLU* 1.3 70.4 - - - +
40B ARG* 1.3 64.4 + - - +
57B THR* 4.0 20.4 - - + +
127B ARG* 3.5 20.9 + - - -
128B GLY 2.8 24.8 + - - +
129B ASN 4.4 1.8 + - - -
131B LEU* 3.7 25.2 - - + +
159B ILE* 4.1 10.5 - - - -
395B LEU* 3.3 17.5 - - - +
396B ASN 3.7 1.3 - - - -
397B CYS* 3.8 25.4 - - - -
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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