Contacts of the strand formed by residues 199 - 208 (chain C) in PDB entry 1F15
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 199 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LYS* 4.8 1.2 - - - -
77C PRO* 4.2 14.3 - - + +
111C VAL* 3.3 37.0 - - + -
112C ASN 3.8 6.5 - - - +
113C PRO* 4.5 2.7 - - + -
114C LEU* 5.1 0.2 - - - -
117C PHE* 3.3 45.5 - - + -
121C VAL* 4.3 14.1 - - + -
153C TYR* 4.8 0.7 - - + -
187C VAL* 5.0 3.1 - - + -
194C LEU* 4.1 26.8 - - + +
195C GLU 5.2 0.4 + - - -
196C THR 4.3 10.7 + - - +
197C ASP* 4.9 0.9 - - - +
198C GLU* 1.3 81.9 - - - +
200C VAL* 1.3 71.0 + - - +
201C LEU* 4.3 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 3.9 18.2 - - + -
75C LEU 4.3 3.6 - - - +
76C LYS* 3.8 37.5 - - + +
77C PRO* 4.9 0.7 - - - -
111C VAL* 4.9 0.2 - - - -
112C ASN* 3.1 39.5 + - + +
114C LEU* 4.4 22.9 - - + -
197C ASP* 4.9 2.9 - - - +
199C LEU* 1.3 81.3 - - - +
201C LEU* 1.3 62.5 + - - +
202C HIS* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 3.7 1.6 - - - +
75C LEU* 3.0 47.2 + - + +
77C PRO* 3.8 31.2 - - + -
109C ILE* 4.1 15.5 - - + -
110C ARG 3.4 6.3 - - - +
111C VAL* 3.7 28.0 - - + -
123C VAL* 4.5 5.2 - - + -
185C VAL* 4.7 6.3 - - + -
187C VAL* 4.0 28.3 - - + -
199C LEU* 4.3 13.0 - - + -
200C VAL* 1.3 73.3 - - - +
202C HIS* 1.3 74.3 + - - +
203C VAL* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C SER* 5.5 3.1 - - - -
73C ILE 3.2 8.5 - - - +
74C THR* 3.7 24.6 + - - +
108C GLN 3.9 0.2 - - - +
109C ILE* 3.4 5.5 - - - +
110C ARG* 2.9 73.0 + - + +
112C ASN* 3.4 24.3 + - + -
200C VAL* 3.6 26.0 - - + +
201C LEU* 1.3 76.1 - - - +
203C VAL* 1.3 68.0 + - - +
204C ASP* 4.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C THR 3.9 0.3 - - - +
72C SER* 3.2 2.1 - - - -
73C ILE* 2.7 45.3 + - + +
75C LEU* 3.9 27.4 - - + -
90C LEU* 3.5 32.8 - - + -
107C LEU* 4.6 3.6 - - + -
108C GLN 3.6 5.2 - - - +
109C ILE* 3.8 24.5 - - + -
185C VAL* 4.9 5.6 - - + -
201C LEU* 5.7 1.1 - - + -
202C HIS* 1.3 78.6 - - - +
204C ASP* 1.3 60.4 + - - +
205C ILE* 3.9 19.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PHE* 4.2 17.9 - - + -
71C THR 3.7 4.5 - - - -
72C SER* 3.2 16.3 + - - +
107C LEU* 3.5 3.1 - - - -
108C GLN* 2.8 67.2 + - + +
110C ARG* 2.8 36.9 + - - -
202C HIS* 4.1 1.4 - - - +
203C VAL* 1.3 75.0 - - - +
205C ILE* 1.3 58.5 - - - +
206C GLU 4.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PHE* 3.9 2.7 - - - -
71C THR* 2.9 24.3 + - - +
73C ILE* 4.2 3.1 - - + -
90C LEU* 4.0 21.8 - - + -
92C LEU* 3.8 27.4 - - + -
104C VAL* 3.6 31.6 - - + -
106C ARG 4.2 2.9 - - - -
107C LEU* 4.5 5.4 - - + -
180C MET* 3.8 30.1 - - + -
203C VAL* 4.0 13.7 - - + +
204C ASP* 1.3 76.7 - - - +
206C GLU* 1.3 61.6 + - - +
207C HIS* 3.3 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C CYS* 3.3 11.6 - - - +
65C ARG* 2.7 26.0 + - - +
68C TYR* 3.9 8.5 - - + +
69C THR 3.3 17.5 - - - +
70C PHE* 3.9 7.3 - - + +
104C VAL* 3.1 8.5 - - - +
105C SER* 2.5 47.9 + - - +
106C ARG* 2.6 61.5 + - - +
204C ASP 4.0 2.0 + - - -
205C ILE* 1.3 69.0 - - - +
207C HIS* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 3.2 7.4 - - - -
69C THR* 2.7 42.4 + - - +
71C THR* 3.0 38.7 + - + +
92C LEU* 4.4 4.9 - - + -
96C VAL* 3.8 18.6 - - + +
102C LYS 5.0 0.2 - - - +
103C LEU 3.1 14.8 - - - +
104C VAL* 4.0 10.1 - - + -
177C ILE* 4.2 15.1 - - + +
205C ILE* 3.3 22.4 - - + -
206C GLU* 1.3 76.3 - - - +
208C GLN* 1.3 82.3 + - - +
210C ILE* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLY 3.7 8.3 - - - +
68C TYR* 3.1 29.9 + - + +
101C LYS 4.2 2.1 - - - +
102C LYS* 3.4 29.0 - - + +
103C LEU* 2.5 60.2 + - - +
207C HIS* 1.3 93.0 + - - +
209C ARG* 1.3 64.5 + - - +
210C ILE* 3.6 1.2 + - - +
----------------------------------------------------------
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