Contacts of the strand formed by residues 35 - 43 (chain A) in PDB entry 3HPN
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 MET 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.4 3.5 - - - -
32A MET 2.8 33.8 + - - +
33A ASN 3.0 1.8 + - - -
34A ASP* 1.3 79.4 - - - +
36A PRO* 1.3 81.9 - - + +
37A ILE* 3.4 3.4 + - + +
76B ARG* 3.3 36.3 - - - +
126B SER 6.1 0.7 - - - +
129B PHE* 3.5 50.5 - - + -
130B GLU* 6.4 1.8 - - - -
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Residues in contact with PRO 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLN* 3.8 28.0 - - + +
30A ASN 3.5 5.8 - - - +
31A ILE* 4.6 2.7 - - + -
34A ASP 3.4 9.2 - - - +
35A MET* 1.3 97.3 - - + +
37A ILE* 1.3 59.9 + - - +
38A TYR* 4.0 19.2 + - + +
132B ARG* 4.7 4.0 + - - -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A MET 4.0 0.3 - - - +
29A GLN* 3.7 0.4 - - - -
30A ASN* 2.6 63.9 + - + +
31A ILE 4.2 0.9 - - - +
32A MET* 4.3 15.3 - - + +
35A MET* 3.9 8.5 - - + +
36A PRO* 1.3 73.9 - - - +
38A TYR* 1.3 60.9 + - - +
39A MET* 4.1 7.0 - - + +
165A LEU* 4.4 13.7 - - + -
32B MET* 5.8 1.8 - - + -
129B PHE* 5.4 8.5 - - + +
132B ARG* 3.4 43.7 - - + +
134B VAL* 5.6 10.3 - - + -
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Residues in contact with TYR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.3 13.7 - - + +
8A ALA* 6.5 0.2 - - - -
13A GLU* 3.7 54.6 + - + -
27A LEU* 3.9 17.7 - - + -
28A MET 3.3 15.0 - - - -
29A GLN* 2.9 32.3 + - + -
36A PRO* 4.0 25.8 - - + +
37A ILE* 1.3 76.9 - - - +
39A MET* 1.3 63.5 + - - +
165A LEU 3.7 0.3 - - - +
132B ARG* 2.7 33.3 + - - +
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Residues in contact with MET 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.7 3.6 - - - -
26A ASP 3.5 0.7 - - - +
27A LEU* 3.4 9.2 - - - +
28A MET* 3.0 47.0 + - + +
30A ASN* 3.0 36.3 - - + +
37A ILE* 4.1 16.4 - - + +
38A TYR* 1.3 75.1 - - - +
40A TYR* 1.3 59.5 + - - +
41A SER* 4.3 13.7 - - - -
163A ALA* 4.1 7.4 - - - -
164A LEU 3.3 15.7 - - - +
165A LEU* 3.3 28.7 - - + -
31B ILE 4.2 6.1 - - - +
32B MET* 3.5 24.0 - - + +
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.7 26.6 - + - -
13A GLU 4.1 8.6 + - - -
16A TRP* 3.5 35.1 + + + +
18A THR* 4.0 13.0 - - + +
25A TRP* 3.5 11.7 - - + -
26A ASP 3.7 18.6 - - - -
27A LEU* 3.7 40.0 - - + +
39A MET* 1.3 72.1 - - - +
41A SER* 1.3 59.0 + - - +
54A LEU* 3.6 48.5 - - + -
164A LEU* 2.7 46.9 + - + +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY 3.8 0.3 - - - +
25A TRP* 3.5 2.8 - - - -
26A ASP* 2.9 36.6 + - - +
28A MET* 3.7 32.7 - - - +
39A MET* 4.3 11.1 - - - -
40A TYR* 1.3 76.5 - - - +
42A VAL* 1.3 67.7 + - - +
43A CYS* 5.8 1.0 - - - +
162A VAL 3.4 11.3 + - - -
163A ALA* 4.3 8.7 - - - +
33B ASN* 4.9 11.6 + - - -
34B ASP* 5.3 3.3 + - - -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY* 3.5 34.8 - - - +
25A TRP* 3.9 22.0 - - + +
28A MET* 5.9 0.4 - - - -
41A SER* 1.3 78.3 + - - +
43A CYS* 1.3 65.8 + - - +
44A ASN* 4.2 12.3 - - - +
52A ASN* 4.0 2.9 - - - +
157A ASP* 3.4 46.7 - - + +
160A ALA 3.2 2.5 - - - +
161A CYS* 3.3 1.0 - - - -
162A VAL* 3.0 34.8 + - + +
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Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER* 5.8 1.3 - - - +
42A VAL* 1.3 73.9 - - - +
44A ASN* 1.3 69.4 + - - +
45A VAL* 3.2 10.5 + - - +
81A PHE* 3.6 22.4 - - - -
160A ALA 3.7 5.4 - - - -
161A CYS* 2.1 46.4 - - - -
33B ASN* 5.2 0.7 - - - -
34B ASP* 3.8 35.8 - - - +
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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