Contacts of the strand formed by residues 39 - 48 (chain X) in PDB entry 2PKA
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 SER 39 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34X TYR* 3.4 5.8 - - - -
35X HIS 2.9 31.4 + - - +
36X TYR 4.1 4.7 + - - -
38X SER* 1.3 81.5 + - - +
40X PHE* 1.3 67.4 - - - +
41X GLN* 3.3 3.5 + - - +
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Residues in contact with PHE 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X ALA* 3.8 19.3 - - + -
33X ILE 3.9 2.2 - - - -
34X TYR* 3.2 31.9 - + + +
39X SER* 1.3 74.2 - - - +
41X GLN* 1.3 75.0 + - - +
42X CYS 3.6 29.4 - - - -
43X GLY* 4.2 0.7 - - - -
73X LEU* 4.0 20.2 - - + -
141Y TRP* 3.8 41.3 - + + -
142Y GLY* 5.1 0.2 - - - -
151Y PHE* 5.6 6.3 - + + -
193Y GLY* 3.6 24.0 - - - -
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Residues in contact with GLN 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X ILE 2.8 14.9 + - - +
35X HIS* 3.2 47.9 - - + +
39X SER* 3.3 8.0 + - - +
40X PHE* 1.3 86.4 + - - +
42X CYS* 1.3 71.6 - - + +
58X CYS* 5.4 0.7 - - - -
193Y GLY* 3.7 18.9 - - - -
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Residues in contact with CYS 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X ILE* 2.8 38.9 + - + +
40X PHE* 3.6 13.4 - - - -
41X GLN* 1.3 96.3 - - - +
43X GLY* 1.3 63.6 + - - +
54X THR* 4.2 0.7 - - - +
57X HIS* 5.0 2.0 - - - -
58X CYS* 2.0 54.1 - - + -
193Y GLY 3.7 4.5 - - - -
195Y SER* 3.1 14.8 - - - +
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Residues in contact with GLY 43 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X GLN* 3.9 9.6 - - - -
31X VAL 3.4 11.4 - - - -
33X ILE* 3.5 5.0 - - - +
40X PHE* 4.2 3.1 - - - -
42X CYS* 1.3 79.3 - - - +
44X GLY* 1.3 52.4 + - - -
54X THR* 2.6 27.9 + - - -
141Y TRP* 5.8 0.7 - - - -
193Y GLY 3.6 6.6 + - - -
194Y ASP 4.6 2.2 - - - -
195Y SER 2.9 11.7 + - - +
196Y GLY* 3.5 7.7 - - - -
197Y GLY* 4.1 4.9 - - - -
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Residues in contact with GLY 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X GLN* 3.6 12.0 + - - +
31X VAL* 3.0 33.5 + - - -
33X ILE* 4.2 6.5 - - - -
43X GLY* 1.3 74.2 - - - -
45X VAL* 1.3 69.9 + - - +
52X VAL* 4.4 0.7 - - - -
53X LEU 3.3 8.5 - - - -
54X THR* 4.2 1.1 - - - -
196Y GLY 3.3 9.9 + - - -
197Y GLY 3.9 0.2 - - - +
198Y PRO* 4.1 1.0 - - - +
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Residues in contact with VAL 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X TRP* 3.3 15.3 - - + +
31X VAL* 3.9 4.9 - - - +
44X GLY* 1.3 80.3 - - - +
46X LEU* 1.3 65.0 + - - +
47X VAL 3.2 1.2 + - - -
52X VAL* 3.5 0.4 - - - -
53X LEU* 2.7 38.5 + - - +
121Y LEU* 3.5 41.1 - - + -
196Y GLY 3.9 6.7 - - - +
197Y GLY 4.1 0.2 - - - -
198Y PRO* 3.5 30.7 - - + -
209Y TRP* 3.7 30.0 - - + +
212Y ILE* 4.4 1.1 - - + -
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Residues in contact with LEU 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X PRO 5.1 0.7 - - - +
29X TRP* 2.9 18.2 + - - +
31X VAL* 3.6 7.4 - - + +
45X VAL* 1.3 69.7 - - - +
47X VAL* 1.3 58.1 + - - +
48X ASN 3.2 22.4 - - - +
49X PRO* 4.5 2.0 - - + -
51X TRP 3.5 8.3 - - - +
52X VAL* 4.3 13.2 - - + +
67X LEU* 4.4 13.7 - - + -
108Y LEU* 4.4 14.1 - - + -
112Y ALA* 4.5 2.9 - - + -
114Y ILE* 4.3 7.2 - - + -
118Y VAL* 4.0 23.3 - - + -
119Y LYS 3.7 24.0 - - - +
120Y VAL* 3.6 17.0 - - + -
121Y LEU* 3.1 27.9 + - - +
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Residues in contact with VAL 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X VAL 3.2 1.8 + - - -
46X LEU* 1.3 73.9 - - - +
48X ASN* 1.3 59.9 + - - +
51X TRP* 2.9 31.4 + - + +
53X LEU* 3.9 20.2 - - + +
105Y LEU* 3.9 14.4 - - + -
120Y VAL* 3.1 20.0 - - - +
121Y LEU 4.3 3.7 - - - +
123Y LEU* 3.8 17.7 - - + -
209Y TRP* 3.7 31.9 - - + -
238Y ILE* 4.7 7.4 - - + -
242Y ILE* 4.1 9.2 - - + +
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Residues in contact with ASN 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X LEU* 3.2 8.6 - - - +
47X VAL* 1.3 77.8 - - - +
49X PRO* 1.3 74.1 - - - +
50X LYS* 2.9 34.4 - - - +
51X TRP* 2.8 52.6 + - + +
120Y VAL* 3.9 4.9 - - - -
242Y ILE* 4.4 18.4 - - + +
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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