Contacts of the strand formed by residues 112 - 121 (chain A) in PDB entry 1F0C
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 PHE 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PRO* 4.3 12.8 - - + -
103A ASP* 3.8 18.8 + - + +
110A ILE 5.4 0.2 - - - -
111A SER* 1.3 79.8 - - - +
113A LYS* 1.3 61.9 + - - +
114A SER* 4.2 17.9 - - - -
188A VAL* 3.7 29.2 - - + -
189A TYR 3.5 9.6 - - - -
190A PHE* 4.1 10.5 - - + -
376B HIS* 4.2 14.4 - + - +
381B LYS* 4.3 13.7 - - - -
383B LEU* 3.9 47.8 - - + -
384B PHE* 3.8 26.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SER 5.6 0.7 - - - +
112A PHE* 1.3 77.9 - - - +
114A SER* 1.3 61.8 + - - +
163A ILE 5.0 0.2 + - - -
164A PHE* 3.1 55.2 + - + +
166A GLU* 3.5 18.8 + - - -
188A VAL* 3.2 3.6 - - - +
189A TYR* 2.8 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 4.2 12.5 - - - -
113A LYS* 1.3 75.5 - - - +
115A MET* 1.3 63.7 + - - +
116A ASN* 5.6 3.8 + - - -
164A PHE* 3.6 6.2 - - - -
186A SER* 5.9 0.2 - - - -
187A ALA 3.2 5.8 - - - -
188A VAL* 3.5 22.4 - - - -
381B LYS* 5.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 1.3 76.6 - - - +
116A ASN* 1.3 67.2 + - - +
117A LYS* 4.2 26.0 - - + -
160A CYS* 4.2 26.0 - - - +
161A VAL* 4.2 12.8 - - + -
164A PHE* 3.5 50.5 - - + -
185A ILE* 4.0 4.2 - - + +
186A SER* 3.5 0.9 - - - -
187A ALA* 2.9 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 2.7 34.1 + - - -
63A ILE* 4.7 21.3 - - + +
114A SER* 5.6 3.1 + - - -
115A MET* 1.3 84.3 + - - +
117A LYS* 1.3 67.5 + - - +
141A ASN* 2.7 43.1 + - + +
185A ILE 3.3 7.4 - - - +
186A SER* 3.6 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 5.7 0.3 - - - +
115A MET* 4.2 20.6 - - + -
116A ASN* 1.3 77.7 - - - +
118A VAL* 1.3 67.3 - - - +
119A TYR* 3.6 30.1 + - + +
136A ASP 5.9 0.9 - - - -
141A ASN* 3.6 15.9 - - - +
143A GLN* 4.3 20.6 + - + +
160A CYS* 3.6 26.4 - - - -
183A LEU 3.8 1.1 - - - +
185A ILE* 2.8 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.9 33.7 - - + -
116A ASN 5.2 0.2 - - - -
117A LYS* 1.3 82.7 - - - +
119A TYR* 1.3 60.8 + - - +
120A GLY 4.1 0.2 - - - -
130A PHE* 4.5 9.0 - - + -
134A ILE* 4.2 13.9 - - + -
141A ASN* 2.8 17.1 + - + +
142A PHE* 3.5 15.3 - - + -
143A GLN* 2.9 29.1 + - - +
182A LEU* 3.3 35.0 - - + -
183A LEU 3.3 6.5 - - - +
184A ALA* 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 3.6 41.7 + - + +
118A VAL* 1.3 74.1 - - - +
120A GLY* 1.3 59.4 + - - +
143A GLN* 3.1 33.0 - - + +
145A VAL* 3.8 33.7 - - + -
147A PHE* 3.5 8.9 - - + -
156A ALA 5.3 0.2 + - - -
157A ILE* 3.8 51.7 + - + +
160A CYS* 4.4 9.2 - - - +
161A VAL* 6.0 0.7 - - - +
182A LEU* 2.8 20.1 - - - +
183A LEU* 2.8 36.7 + - + +
185A ILE* 4.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 1.3 73.7 - - - +
121A ARG* 1.3 65.9 + - - -
126A PHE* 3.6 14.4 - - - -
142A PHE* 3.9 6.3 - - - -
143A GLN 2.6 15.2 + - - -
144A THR* 3.4 3.4 - - - -
145A VAL* 2.8 26.3 + - - +
147A PHE* 4.0 3.1 - - - -
181A CYS 3.7 0.2 - - - -
182A LEU* 3.5 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY* 1.3 72.0 - - - -
122A TYR* 1.3 71.1 + - + +
123A SER* 3.6 23.4 + - - +
124A ALA* 2.9 33.2 + - + +
126A PHE* 3.7 8.0 - - - -
145A VAL 3.5 7.2 - - - +
147A PHE* 3.5 17.6 - - + +
179A PRO 4.1 15.1 + - - -
180A THR 3.0 25.1 + - - +
181A CYS* 2.9 42.2 + - - +
325A SER* 4.5 0.8 + - - -
358A CYS* 2.6 51.7 - - - +
359A ALA* 5.2 2.6 + - - +
----------------------------------------------------------
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