Contacts of the strand formed by residues 125 - 131 (chain A) in PDB entry 5F2R
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 LYS 125 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY* 6.2 2.9 - - - +
101A ARG 3.9 14.6 - - - +
102A THR* 4.9 1.6 - - + -
103A TRP* 3.7 4.5 - - - +
120A VAL 3.2 1.6 - - - +
121A GLU* 3.4 3.1 - - - -
122A LYS 2.8 32.7 + - - +
123A LYS* 3.7 13.9 - - + +
124A THR* 1.3 88.4 - - - +
126A PRO* 1.4 66.8 - - + +
127A TYR* 3.2 27.1 + - + -
141A ALA* 4.6 2.0 - - - +
142A PRO* 4.9 3.1 - - + -
143A GLU* 2.6 38.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.1 20.9 - - + +
101A ARG 3.2 21.5 - - - +
103A TRP* 3.7 11.6 - - + +
108A VAL* 3.8 29.4 - - + -
119A VAL* 3.5 21.8 - - + +
120A VAL 3.6 5.8 - - - +
125A LYS* 1.4 83.1 - - + +
127A TYR* 1.3 64.0 - - - +
128A ILE* 4.0 3.3 - - - +
142A PRO* 3.2 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 3.3 4.3 - - - -
120A VAL* 2.8 41.2 + - + +
122A LYS* 3.4 54.5 - - + -
123A LYS* 4.3 15.7 - - + +
125A LYS* 4.0 23.1 + - + -
126A PRO* 1.3 76.5 - - - +
128A ILE* 1.3 60.6 + - - +
139A THR* 3.4 32.3 - - + -
140A PHE 3.4 6.1 - - - -
141A ALA* 3.5 39.7 - - + +
142A PRO* 4.5 0.7 - - - -
144A GLU* 4.2 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 3.8 29.4 - - + -
95A ALA* 5.0 4.5 - - + -
98A LEU* 4.1 12.3 - - + -
117A PHE* 3.6 39.5 - - + -
118A LYS 3.4 3.6 - - - +
119A VAL* 4.4 1.6 - - + -
126A PRO 4.0 9.6 - - - +
127A TYR* 1.3 72.4 - - - +
129A GLN* 1.3 60.9 + - - +
130A VAL* 4.1 8.6 + - + -
138A LYS 3.7 0.9 - - - +
139A THR* 3.2 3.5 - - - -
140A PHE* 2.8 52.1 + - + +
142A PRO* 3.9 25.8 - - + -
145A ILE* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU 4.6 1.0 - - - +
118A LYS* 2.9 63.1 + - + +
120A VAL* 3.8 30.0 - - + +
127A TYR 4.0 0.6 + - - -
128A ILE* 1.3 71.8 - - - +
130A VAL* 1.3 73.1 + - - +
131A ASP* 5.2 1.4 - - - +
137A THR* 3.5 28.5 - - + +
138A LYS 3.3 5.4 - - - +
139A THR* 3.8 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.1 17.3 - - + -
89A GLU 3.7 19.1 - - - +
90A ASN* 3.8 13.9 - - - +
92A VAL* 3.9 24.7 - - + -
117A PHE* 4.4 2.2 - - + -
118A LYS* 6.0 0.9 - - - +
128A ILE* 4.1 6.3 - - + -
129A GLN* 1.3 81.4 - - - +
131A ASP* 1.3 65.1 + - - +
132A ILE* 4.0 5.7 + - + +
136A GLN 3.9 0.2 - - - +
137A THR* 3.4 3.2 - - - -
138A LYS 2.8 35.5 + - - +
140A PHE* 4.0 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.6 2.1 - - - +
90A ASN* 2.9 43.9 + - - +
118A LYS* 6.0 2.3 - - - -
129A GLN* 5.2 1.4 - - - +
130A VAL* 1.3 72.5 - - - +
132A ILE* 1.3 62.0 + - - +
133A GLY 3.7 2.5 - - - +
135A GLY* 4.1 19.7 - - - +
136A GLN 3.3 7.0 - - - +
137A THR* 3.0 28.8 + - - +
----------------------------------------------------------
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