Contacts of the strand formed by residues 129 - 139 (chain A) in PDB entry 1F11
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 GLY 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLN* 3.1 33.6 + - - +
125A LEU* 3.2 17.5 + - - +
127A SER 3.3 5.6 - - - -
128A GLY* 1.3 80.4 - - - +
130A ALA* 1.3 61.3 + - - -
181A LEU 4.2 2.7 - - - -
182A THR* 4.7 0.2 - - - -
183A LYS 4.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 3.8 10.3 - - + -
124A GLN* 3.8 2.1 - - - +
125A LEU* 3.6 12.6 - - + -
129A GLY* 1.3 73.5 - - - +
131A SER* 1.3 61.8 + - - +
132A VAL 4.0 0.3 + - - -
179A LEU 4.0 0.9 - - - +
180A THR* 3.8 0.8 - - - +
181A LEU* 2.8 46.8 + - + +
182A THR 4.0 4.5 - - - +
183A LYS 4.2 0.2 - - - +
186A TYR* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE 4.2 0.2 - - - +
119A PRO 4.2 1.6 - - - -
120A PRO* 3.7 18.8 - - - +
124A GLN* 3.0 32.5 + - - +
130A ALA* 1.3 71.8 - - - +
132A VAL* 1.3 63.4 + - - +
133A VAL* 3.7 5.8 + - - +
178A THR* 4.2 8.9 - - - +
179A LEU 3.5 4.5 - - - -
180A THR* 3.3 24.6 + - - +
124B LEU* 5.5 2.9 - - - +
143B LEU* 4.0 17.8 - - - +
145B LYS* 4.1 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 4.0 5.2 - - + -
118A PHE 3.3 16.8 - - - +
120A PRO* 4.3 17.9 - - + -
130A ALA 5.0 0.2 - - - +
131A SER* 1.3 74.1 - - - +
133A VAL* 1.3 59.4 + - - +
148A TRP* 3.4 33.3 - - + -
178A THR* 3.5 2.4 - - - -
179A LEU* 2.9 39.4 + - + +
181A LEU* 4.6 8.3 - - + -
186A TYR* 4.4 13.7 - - + -
192A TYR* 4.5 15.0 - - + -
209A PHE* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.5 1.7 - - - +
118A PHE* 2.7 42.0 + - + -
131A SER 3.7 6.0 + - - +
132A VAL* 1.3 71.3 - - - +
134A CYS* 1.3 64.0 + - - +
135A PHE* 3.8 38.4 - - + -
148A TRP* 4.4 1.6 - - - -
176A SER* 5.5 0.7 - - - +
177A SER 3.7 6.5 - - - +
178A THR* 3.6 27.4 - - + +
124B LEU* 3.7 26.9 - - + +
143B LEU* 4.4 20.0 - - + -
188B SER* 5.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.3 25.8 - - - -
116A SER 3.5 5.2 - - - -
117A ILE* 4.5 4.0 - - + -
133A VAL* 1.3 74.0 - - - +
135A PHE* 1.3 64.8 + - - +
136A LEU* 3.8 9.4 - - + +
148A TRP* 3.5 16.1 - - + -
176A SER* 3.4 3.5 - - - -
177A SER* 2.8 40.5 + - - +
194A CYS* 2.0 49.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR 3.1 16.1 - - - +
115A VAL* 3.2 1.9 - - - -
116A SER* 2.9 31.3 + - - +
118A PHE* 3.4 28.3 - + - -
133A VAL* 3.8 19.3 - - + -
134A CYS* 1.3 73.2 - - - +
136A LEU* 1.3 61.6 + - - +
137A ASN* 3.7 13.2 - - - +
175A MET 3.8 0.7 - - - -
176A SER* 3.8 9.9 - - - -
124B LEU* 4.4 3.4 - - + -
139B THR* 4.4 3.4 - - + -
141B GLY* 3.7 19.1 - - - -
174B PHE* 3.7 32.5 - + - -
188B SER* 3.8 20.9 - - - -
189B SER 3.8 12.3 - - - -
190B SER* 3.5 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 4.1 12.1 - - + -
114A THR 4.1 3.4 - - - -
115A VAL* 4.3 11.4 - - + -
134A CYS* 3.8 26.7 - - + +
135A PHE* 1.3 75.7 - - - +
137A ASN* 1.3 61.7 + - - +
139A PHE* 3.3 14.2 - - + -
144A ILE* 4.3 11.4 - - + -
145A ASN 4.3 1.1 - - - +
146A VAL* 3.3 28.5 - - + -
175A MET* 2.8 58.0 + - + +
177A SER* 4.7 1.3 - - - +
194A CYS* 4.7 1.1 - - - -
196A ALA* 3.5 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 3.2 3.1 - - - +
114A THR* 2.9 44.1 + - - +
116A SER* 5.3 0.6 + - - -
135A PHE* 4.1 11.8 - - - +
136A LEU* 1.3 76.7 - - - +
138A ASN* 1.3 81.6 + - - +
139A PHE 3.6 0.9 - - - -
174A SER* 3.5 10.0 + - - -
139B THR* 4.6 11.9 + - - +
172B HIS* 4.0 13.5 - - - +
174B PHE* 3.8 19.8 - - - -
190B SER* 3.8 16.0 + - - -
192B THR* 4.3 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 4.0 10.0 - - - +
112A ALA 3.5 11.1 - - - +
114A THR* 5.5 3.9 + - - +
137A ASN* 1.3 79.3 - - - +
139A PHE* 1.3 59.1 + - - +
170A ASP* 4.2 11.5 + - - +
172A THR* 3.5 25.4 + - + +
173A TYR 3.1 9.0 + - - -
174A SER* 2.9 7.3 + - - -
172B HIS* 3.0 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 3.2 16.2 - - - +
113A PRO* 3.6 27.1 - - + -
136A LEU* 3.3 28.7 - - + -
138A ASN* 1.3 73.9 - - - +
140A TYR* 1.3 66.6 + - - +
141A PRO 3.2 20.2 - - - -
142A LYS* 3.4 29.2 - - - -
144A ILE* 3.6 33.7 - - + -
163A TRP* 4.2 6.3 - + - -
172A THR* 3.4 4.1 - - - -
173A TYR* 2.8 42.6 + - + +
174A SER* 3.5 14.8 - - - -
175A MET* 3.6 16.6 - - + -
198A HIS* 4.2 1.3 - + - +
----------------------------------------------------------
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