Contacts of the strand formed by residues 35 - 43 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE* 3.4 2.3 - - - -
32C MET 2.9 32.3 + - - +
33C ASN 2.9 4.3 + - - +
34C ASP* 1.3 79.9 - - - +
36C PRO* 1.3 82.9 - - + +
37C ILE* 3.3 5.3 + - + +
76D ARG* 3.3 35.9 - - - +
126D SER 6.1 0.7 - - - +
129D PHE* 3.8 44.0 - - + -
130D GLU* 6.1 2.9 - - - +
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Residues in contact with PRO 36 (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 GLN* 3.9 20.4 - - - +
30C ASN 3.5 6.3 - - - +
31C ILE* 4.6 2.6 - - + -
34C ASP 3.4 9.2 - - - +
35C MET* 1.3 96.1 - - + +
37C ILE* 1.3 60.8 + - - +
38C TYR* 3.8 28.7 + - + +
129D PHE* 6.1 0.9 - - - +
132D ARG* 5.0 1.2 + - - -
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Residues in contact with ILE 37 (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 GLN* 4.4 0.4 - - - +
30C ASN* 2.7 56.1 + - + +
31C ILE 4.4 0.2 - - - +
32C MET* 4.1 17.9 - - + +
35C MET* 3.5 15.3 - - + +
36C PRO* 1.3 72.5 - - - +
38C TYR* 1.3 63.2 + - - +
39C MET* 4.0 10.4 - - + +
165C LEU* 4.5 11.2 - - + -
32D MET* 6.1 1.3 - - + -
129D PHE* 4.9 8.7 - - + +
132D ARG* 3.1 44.6 - - - +
134D VAL* 5.6 8.7 - - + -
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Residues in contact with TYR 38 (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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7C PHE* 3.3 22.3 - - + +
13C GLU* 3.8 45.8 + - + -
27C LEU* 4.0 16.8 - - + -
28C MET 3.3 15.7 - - - -
29C GLN* 2.8 33.7 + - + -
36C PRO* 3.8 27.7 + - + +
37C ILE* 1.3 76.1 - - - +
39C MET* 1.3 63.9 + - - +
165C LEU* 3.8 2.1 - - - +
132D ARG* 3.0 25.8 + - - +
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Residues in contact with MET 39 (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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7C PHE* 3.7 7.6 - - - -
26C ASP 3.6 0.5 - - - +
27C LEU* 3.3 6.2 - - - +
28C MET* 3.0 48.2 + - + +
30C ASN* 3.0 38.6 - - + +
37C ILE* 4.0 16.8 - - + +
38C TYR* 1.3 77.0 - - - +
40C TYR* 1.3 59.6 + - - +
41C SER* 4.4 13.2 - - - -
163C ALA* 4.3 7.0 - - + -
164C LEU 3.3 17.3 - - - +
165C LEU* 3.4 28.7 - - + -
31D ILE 4.4 5.8 - - - +
32D MET* 3.7 19.5 - - + +
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Residues in contact with TYR 40 (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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7C PHE* 3.7 25.1 - + - -
13C GLU 4.2 5.1 + - - -
16C TRP* 3.6 34.7 + + + +
18C THR* 4.1 11.9 - - + +
25C TRP* 3.6 12.9 - - + -
26C ASP* 3.6 9.9 - - - -
27C LEU* 3.5 52.6 - - + +
39C MET* 1.3 70.8 - - - +
41C SER* 1.3 61.3 + - - +
54C LEU* 3.6 49.8 - - + -
163C ALA* 3.6 0.2 - - - -
164C LEU* 2.7 46.0 + - + +
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Residues in contact with SER 41 (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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24C GLY 3.9 0.5 - - - +
25C TRP* 3.5 3.5 - - - -
26C ASP* 2.9 36.9 + - - +
28C MET* 3.6 33.0 - - - +
39C MET* 4.4 11.0 - - - -
40C TYR* 1.3 78.0 - - - +
42C VAL* 1.3 66.3 + - - +
43C CYS* 5.8 0.7 - - - +
162C VAL 3.4 11.6 + - - -
163C ALA* 4.1 8.3 - - - +
33D ASN* 5.0 9.9 + - - -
34D ASP 5.8 0.3 + - - -
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Residues in contact with VAL 42 (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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24C GLY* 3.6 34.3 - - - +
25C TRP* 3.8 22.4 - - + +
28C MET* 5.8 0.4 - - - -
41C SER* 1.3 78.5 + - - +
43C CYS* 1.3 65.2 + - - +
44C ASN* 4.1 15.3 - - - +
52C ASN* 4.2 0.2 - - - +
157C ASP* 3.5 46.0 - - + +
160C ALA 3.2 3.4 - - - +
161C CYS* 3.3 0.9 - - - -
162C VAL* 3.0 34.2 + - + +
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Residues in contact with CYS 43 (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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41C SER* 5.8 1.3 - - - +
42C VAL* 1.3 74.7 - - - +
44C ASN* 1.3 69.2 + - - +
45C VAL* 3.2 9.5 + - - +
81C PHE* 3.7 21.8 - - - -
160C ALA 3.7 5.4 - - - -
161C CYS* 2.1 46.2 - - - -
33D ASN* 5.2 0.7 - - - -
34D ASP* 3.8 33.0 - - - +
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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