Contacts of the strand formed by residues 44 - 52 (chain C) in PDB entry 1P27
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 44 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A HIS* 6.1 1.3 - - - -
36C ASN 3.9 1.2 - - - +
37C ASN* 3.5 5.2 - - - +
38C SER* 3.4 31.6 + - - +
42C ASN* 3.7 18.1 - - + +
43C ASP* 1.3 85.8 - - - +
45C MET* 1.3 69.9 + - - +
46C ILE* 4.8 11.6 - - + +
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Residues in contact with MET 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TYR* 4.7 6.5 - - - +
19A HIS* 2.9 54.1 - - + +
21A PHE* 4.5 7.4 - - + -
37A ASN* 5.7 0.2 - - - +
21C PHE* 4.1 17.3 - - + -
35C ALA* 5.2 1.3 - - - -
36C ASN 3.7 9.4 - - - +
37C ASN* 3.2 35.2 - - + +
44C VAL* 1.3 80.4 - - - +
46C ILE* 1.3 74.9 + - - +
47C ARG* 4.1 13.4 + - + +
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C TYR* 4.2 10.3 - - + -
35C ALA* 3.2 7.1 - - - +
36C ASN* 2.9 56.7 + - + +
44C VAL* 4.8 12.8 - - + -
45C MET* 1.3 78.9 - - - +
47C ARG* 1.3 64.9 + - - +
48C LYS* 4.0 19.3 - - + -
143C ILE* 4.0 24.7 - - + -
144C LYS 4.0 20.6 - - - +
145C PRO 4.7 2.7 - - - -
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TYR* 3.4 46.7 + - - -
21A PHE* 5.7 2.0 - - - -
23A GLU* 3.2 25.7 + - - -
85A ARG* 4.5 13.8 - - - +
87A GLU* 3.0 38.9 + - - +
21C PHE* 6.0 2.0 - - - -
33C ARG* 3.3 18.2 - - - +
34C TYR 3.5 3.4 - - - +
35C ALA* 4.3 20.2 - - + +
45C MET* 4.1 14.0 + - + +
46C ILE* 1.3 78.7 - - - +
48C LYS* 1.3 71.1 + - - +
49C GLU* 5.8 0.2 - - - -
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Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 4.5 0.2 - - - -
33C ARG* 3.4 3.3 - - - +
34C TYR* 2.8 40.3 + - + +
46C ILE* 4.0 22.4 - - + -
47C ARG* 1.3 84.1 + - - +
49C GLU* 1.3 67.0 + - - +
137C ILE* 4.4 14.4 - - + -
141C PHE* 3.7 57.8 - - + -
143C ILE* 4.8 10.5 - - + -
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.3 7.3 + - - -
87A GLU* 4.7 5.6 - - - +
31C LYS* 2.7 35.2 + - + +
32C LEU 3.2 7.2 - - - +
33C ARG* 3.2 37.2 + - + +
47C ARG 5.8 0.4 - - - -
48C LYS* 1.3 80.7 - - - +
50C ALA* 1.3 61.9 + - - +
137C ILE* 6.1 0.7 - - - -
140C HIS* 5.3 0.3 - - - -
141C PHE* 3.4 15.7 - - - -
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LYS* 3.5 3.3 - - - +
32C LEU* 2.7 47.5 + - + +
49C GLU* 1.3 75.8 - - - +
51C TYR* 1.3 63.5 + - - +
137C ILE* 5.9 1.1 - - + +
140C HIS* 4.1 20.4 - - + +
141C PHE* 4.4 5.8 - - + -
150D PHE* 4.0 26.0 - - + -
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Residues in contact with TYR 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 3.5 30.8 + - - +
30C GLY 3.4 4.0 - - - +
31C LYS* 3.5 47.2 - - + -
50C ALA* 1.3 77.0 - - - +
52C VAL* 1.3 61.4 + - - +
150D PHE* 3.4 10.8 - - - +
151D VAL* 3.0 39.7 + - + +
152D ARG 4.2 6.1 - - - -
153D GLY* 3.7 32.8 - - - +
154D PRO* 3.7 23.9 - - + +
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 4.5 7.2 - - + -
29C ASP 5.2 0.7 - - - +
30C GLY* 2.9 29.5 + - - +
32C LEU* 4.4 21.1 - - + -
50C ALA 5.0 0.2 - - - +
51C TYR* 1.3 78.0 - - - +
53C HIS* 1.3 71.6 + - - +
54C LYS* 3.7 1.2 + - - -
56C VAL* 3.9 26.9 - - + -
57C MET* 3.9 24.9 - - + -
136C LEU* 4.5 4.9 - - + -
149D CYS 3.5 6.1 - - - +
150D PHE* 4.1 21.3 - - + -
151D VAL* 4.4 8.4 - - - +
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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