Contacts of the strand formed by residues 109 - 118 (chain A) in PDB entry 5KQF
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 ARG 109 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR 3.9 1.5 + - - +
108A TYR* 1.3 83.2 - - - +
110A ASP* 1.3 63.2 + - - +
111A LEU* 4.8 0.7 - - - +
129A GLY* 3.1 5.2 - - - -
130A THR* 2.8 49.9 + - - +
144A ARG* 3.4 50.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 5.5 1.1 + - - -
108A TYR* 3.3 30.3 + - + +
109A ARG* 1.3 73.3 - - - +
111A LEU* 1.3 62.4 + - - +
112A ARG* 2.7 47.9 + - + +
113A LYS 4.6 0.3 + - - +
127A GLU* 5.7 3.4 - - - +
128A LEU 3.5 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG 3.7 1.3 + - - +
110A ASP* 1.3 75.5 + - - +
112A ARG* 1.3 71.0 + - - +
113A LYS* 3.3 8.1 + - + +
128A LEU* 3.1 29.4 + - + +
129A GLY* 3.8 25.6 - - - +
130A THR* 4.2 9.2 - - + -
146A ASN* 3.7 22.2 - - - +
181A LEU* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASP* 2.7 34.7 + - + +
111A LEU* 1.3 80.4 - - - +
113A LYS* 1.3 56.9 - - - +
128A LEU 4.0 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
110A ASP* 4.6 0.2 + - - -
111A LEU* 3.3 10.7 - - + +
112A ARG* 1.3 78.8 - - - +
114A GLY* 1.3 72.4 - - - +
127A GLU* 3.7 3.6 - - - +
128A LEU* 2.8 46.9 + - + +
177A PRO* 5.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS* 1.3 88.1 - - - +
115A VAL* 1.3 63.2 + - - +
126A GLY 3.3 10.3 - - - -
127A GLU* 4.4 4.0 - - - -
128A LEU* 4.6 1.0 - - - +
177A PRO* 5.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLY* 1.3 75.3 - - - +
116A TYR* 1.3 63.9 + - - +
117A VAL* 3.7 17.7 - - + -
124A TRP* 3.7 23.9 - - + +
125A GLU* 3.3 7.4 - - - +
126A GLY 2.8 40.3 + - - +
128A LEU* 3.8 25.1 - - + -
148A ALA* 4.3 0.7 - - + -
176A ARG* 3.7 10.5 - - + +
177A PRO* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 1.3 76.7 - - - +
117A VAL* 1.3 62.2 + - - +
118A PRO* 3.5 41.1 - - + +
123A LYS* 3.9 29.6 - - + +
124A TRP 3.8 1.8 - - - -
125A GLU* 3.3 31.6 - - + -
176A ARG* 5.2 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 5.9 0.2 - - - +
115A VAL* 3.7 14.4 - - + -
116A TYR* 1.3 78.2 - - - +
118A PRO* 1.3 61.4 - - - +
119A TYR* 3.5 37.7 + - + +
123A LYS* 3.2 4.5 - - - -
124A TRP* 2.8 75.0 + - + +
176A ARG* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 3.5 34.3 - - + +
117A VAL* 1.3 90.1 - - + +
119A TYR* 1.3 73.0 + - - +
122A GLY 4.6 0.7 - - - +
123A LYS* 3.8 10.5 - - + -
176A ARG* 4.7 6.5 + - - -
----------------------------------------------------------
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