Contacts of the strand formed by residues 67 - 75 (chain F) 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 ILE 67 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F LEU* 4.2 15.5 - - + -
64F ALA* 4.0 21.1 - - + -
66F ARG* 1.3 77.6 - - - +
68F PHE* 1.3 60.8 + - - +
69F ILE* 4.3 16.6 - - + -
96F TYR* 6.3 1.3 - - + -
142F SER* 3.2 6.9 - - - -
143F VAL* 3.0 47.7 + - + +
146F LEU* 3.6 27.6 - - + -
151F PHE* 3.6 32.5 - - + -
153F LEU* 4.4 2.5 - - + -
169F VAL* 3.9 13.2 - - + -
170F TYR 3.4 7.0 - - - +
171F TYR* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ARG* 3.9 31.2 - - + -
67F ILE* 1.3 75.5 - - - +
69F ILE* 1.3 61.3 + - - +
140F GLU* 4.0 17.9 - - + -
141F ARG 3.6 2.7 - - - -
142F SER* 3.7 20.6 - - - -
169F VAL* 3.3 4.7 - - - +
170F TYR* 2.6 78.7 + + + +
171F TYR* 4.3 1.1 - - - -
172F LYS* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ILE* 4.3 13.0 - - + -
68F PHE* 1.3 77.6 - - - +
70F GLU* 1.3 60.7 + - - +
71F LEU* 4.0 24.9 + - + +
94F LEU* 4.3 15.5 - - + -
115F ILE* 4.0 10.1 - - + -
139F GLU 3.6 1.9 - - - +
140F GLU* 3.2 7.8 - - - +
141F ARG 2.7 39.0 + - - +
143F VAL* 3.8 28.9 - - + -
153F LEU* 3.8 44.6 - - + -
167F VAL* 4.9 0.7 - - + -
168F ARG 3.5 5.8 - - - +
169F VAL* 4.4 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PHE 4.2 0.2 - - - -
69F ILE* 1.3 73.3 - - - +
71F LEU* 1.3 65.8 + - - +
72F LYS* 3.9 24.3 + - - +
138F VAL* 4.1 21.4 - - + +
139F GLU 3.6 2.9 - - - +
140F GLU* 3.8 20.7 - - + +
166F SER* 3.8 5.0 + - - +
167F VAL* 3.4 6.2 + - - -
168F ARG* 2.7 73.2 + - + +
170F TYR* 4.7 4.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F ILE* 4.0 13.2 - - + +
70F GLU* 1.3 82.6 - - - +
72F LYS* 1.3 62.1 + - - +
73F PHE* 4.0 13.9 - - + -
92F PHE* 4.1 10.3 - - + -
94F LEU* 4.4 9.9 - - + -
118F ILE* 4.0 33.0 - - + -
137F ASN 3.5 0.7 - - - +
138F VAL* 3.3 6.8 - - - +
139F GLU* 2.7 43.3 + - + +
141F ARG* 6.1 0.4 - - + -
155F PHE* 3.7 32.3 - - + -
164F LEU* 4.4 4.0 - - + -
166F SER 3.6 1.1 - - - +
167F VAL* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E GLU 5.2 1.0 + - - +
131E ALA* 2.8 36.1 + - - +
132E ARG* 4.4 2.9 - - + -
133E HIS* 6.0 1.6 - - - -
70F GLU* 3.9 27.1 + - - +
71F LEU* 1.3 77.7 - - - +
73F PHE* 1.3 59.4 + - - +
136F LEU* 4.0 21.7 - - + +
137F ASN 3.1 5.4 - - - +
138F VAL* 4.0 26.5 - - + -
164F LEU* 3.5 3.7 - - - +
165F LEU* 2.7 31.5 + - + -
166F SER* 3.0 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LEU* 4.0 9.9 - - + -
72F LYS* 1.3 79.2 - - - +
74F THR* 1.3 62.0 + - - +
75F VAL* 3.6 26.9 - - + -
92F PHE* 3.6 24.5 - + - -
118F ILE* 3.5 20.6 - - + -
119F ALA 3.9 8.3 - - - -
120F PRO* 3.9 12.3 - - + -
136F LEU* 3.7 4.2 - - - +
137F ASN* 2.8 60.1 + - + +
139F GLU* 3.6 30.5 - - + -
162F VAL* 4.2 4.3 - - + -
163F ALA 3.0 14.8 - - - +
164F LEU* 3.9 12.3 - - + -
165F LEU* 4.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E MET* 3.8 4.2 - - + -
33E ASN* 2.8 28.7 + - - -
73F PHE* 1.3 76.7 - - - +
75F VAL* 1.3 67.2 + - - +
124F THR* 4.5 2.2 - - - -
134F VAL* 3.7 21.3 - - + -
135F LYS 3.2 25.8 - - - +
136F LEU* 4.2 6.7 - - + -
137F ASN* 4.3 0.9 - - - +
162F VAL* 3.3 6.1 - - - +
163F ALA* 2.9 38.8 + - - +
165F LEU* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ASN* 4.2 1.1 - - - -
73F PHE* 3.6 28.3 - - + -
74F THR* 1.3 81.9 - - - +
76F ARG* 1.3 71.2 + - - +
77F ASP 3.6 0.2 + - - -
89F LYS 4.7 1.6 - - - +
90F GLU* 3.9 34.3 - - + +
92F PHE* 5.0 3.1 - - + -
120F PRO* 3.9 22.0 - - + -
122F GLU 5.0 0.2 + - - -
123F ILE* 3.7 4.5 - - + -
124F THR* 2.9 28.8 + - - -
135F LYS 4.8 0.6 + - - -
137F ASN* 4.4 4.8 - - - +
160F ALA* 5.0 2.2 - - + -
161F CYS 3.3 9.6 - - - +
162F VAL* 4.2 11.2 - - + -
----------------------------------------------------------
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