Contacts of the strand formed by residues 17 - 21 (chain A) in PDB entry 3HPD
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 LEU 17 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG 3.7 1.4 + - - +
16A PRO* 1.3 69.6 - - - +
18A VAL* 1.3 58.7 + - - +
40A SER* 3.3 28.5 - - - +
41A PRO 4.2 2.2 - - - +
42A VAL* 3.8 35.4 - - + -
53A MET* 5.3 1.6 - - - +
56A LEU* 3.7 39.7 - - + +
57A ALA* 3.8 7.0 - - - +
58A ASP* 2.8 43.5 + - - +
59A ALA 3.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO* 4.1 11.0 - - + +
17A LEU* 1.3 76.2 - - - +
19A HIS* 1.3 61.3 + - - +
20A ASN* 2.9 24.0 + - - +
34A LEU* 4.0 15.0 - - + -
39A ALA* 4.5 0.2 - - + -
40A SER 2.8 10.8 + - - +
41A PRO* 3.6 1.4 - - - +
42A VAL* 3.2 17.7 + - - -
59A ALA* 3.7 8.5 - - + +
61A VAL* 3.6 30.5 - - + -
199A ALA 4.1 5.6 - - - +
202A GLY* 3.8 13.0 - - - +
203A ALA* 3.6 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.9 1.8 + - - -
18A VAL* 1.3 68.9 - - - +
20A ASN* 1.3 67.5 + - - +
21A ILE* 3.6 16.5 - - + +
42A VAL* 3.4 22.5 - - + +
44A ALA* 2.8 33.3 + - - +
50A LEU* 4.1 9.4 - - + -
53A MET* 4.2 15.7 - - + +
54A ILE* 3.4 36.3 + - + +
57A ALA* 3.6 20.4 - - + -
59A ALA 2.9 11.9 + - - +
60A VAL* 3.3 9.1 - - + +
61A VAL* 2.7 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 2.9 32.1 + - - +
19A HIS* 1.3 74.7 - - - +
21A ILE* 1.3 62.2 + - - +
22A THR* 3.5 11.4 + - + -
27A MET* 6.0 0.2 - - - +
30A THR* 4.4 3.1 + - - -
34A LEU* 3.7 17.1 - - - +
42A VAL 2.8 10.9 + - - +
43A MET* 3.4 38.1 - - + +
44A ALA 3.3 22.9 + - - -
61A VAL* 3.4 27.2 - - - +
199A ALA* 3.9 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 3.6 19.5 - - + +
20A ASN* 1.3 70.3 - - - +
22A THR* 1.3 58.4 + - - +
44A ALA 3.4 16.6 - - - +
45A HIS* 4.3 8.7 - - + -
50A LEU* 4.1 8.5 - - + -
60A VAL* 4.5 8.5 - - + -
61A VAL 2.9 10.8 + - - +
62A ILE* 3.5 5.9 - - + -
63A ASN 3.0 25.0 + - - +
71A TRP* 4.1 22.2 - - + -
74A SER* 4.3 4.9 - - - +
75A MET* 3.6 31.8 - - + +
78A ALA* 3.2 35.4 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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