Contacts of the strand formed by residues 112 - 127 (chain B) in PDB entry 5IXG
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 VAL 112 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU 3.4 2.6 - - - +
108B THR* 3.2 1.3 - - - -
109B LEU 3.0 29.5 + - - +
110B HIS* 3.6 14.6 - - + +
111B GLY* 1.3 79.9 - - - +
113B THR* 1.3 64.4 + - - +
114B LYS* 3.7 22.4 - - + +
148B ASP 3.7 21.8 - - - +
149B PHE* 3.4 25.0 - - - +
150B GLY* 4.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASN* 3.8 29.6 - - + +
107B LEU 3.3 3.8 - - - +
108B THR* 2.7 30.5 + - - +
111B GLY 4.2 1.6 + - - -
112B VAL* 1.3 74.2 - - - +
114B LYS* 1.3 76.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASN* 3.4 6.9 - - - +
107B LEU* 2.9 33.4 + - - +
112B VAL* 3.7 14.3 - - + +
113B THR* 1.3 83.8 - - - +
115B PRO* 1.3 78.3 - - + +
148B ASP* 2.9 45.9 + - + +
149B PHE* 3.6 25.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLY 3.4 11.7 - - - +
106B ASN* 3.6 10.0 - - - +
114B LYS* 1.3 99.0 - - + +
116B LEU* 1.3 62.5 + - - +
144B PHE* 5.9 1.7 - - - +
149B PHE* 5.2 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 2.9 35.7 + - + -
105B GLY 2.9 20.5 + - - +
107B LEU* 3.9 39.0 - - + -
114B LYS 3.5 0.6 + - - -
115B PRO* 1.3 76.5 - - - +
117B THR* 1.4 74.5 + - - +
118B LEU* 4.0 16.2 - - + -
142B GLY* 4.8 0.4 - - - -
143B GLU 3.7 31.6 - - - +
144B PHE* 4.5 9.4 - - + -
149B PHE* 5.7 1.8 - - + -
165B LEU* 4.0 19.5 - - + -
201B OTP 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B SER* 4.4 7.6 - - - -
103B VAL 3.2 12.1 - - - +
104B VAL* 4.0 28.0 - - + +
116B LEU* 1.4 83.1 + - - +
118B LEU* 1.3 76.8 + - - +
119B LYS* 4.2 2.1 + - + +
141B VAL 4.2 0.2 - - - +
142B GLY* 4.0 8.7 - - - -
143B GLU 4.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.7 36.1 - - + +
102B SER* 3.1 5.9 - - - -
103B VAL* 2.8 39.6 + - + +
116B LEU* 4.0 18.8 - - + -
117B THR* 1.3 82.0 - - - +
119B LYS* 1.3 60.6 + - - +
120B ILE* 5.2 0.2 - - - -
140B ALA* 4.6 4.3 - - + -
141B VAL 3.4 4.3 - - - +
142B GLY* 4.0 14.6 - - - -
165B LEU* 4.6 3.1 - - + -
167B ILE* 3.7 31.4 - - + -
201B OTP 4.0 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL 3.7 10.1 - - - +
102B SER* 4.3 2.7 - - - +
117B THR* 4.2 2.8 + - + +
118B LEU* 1.3 73.9 - - - +
120B ILE* 1.3 65.1 + - - +
121B ASP* 2.8 31.5 + - - +
140B ALA* 3.1 4.4 - - - -
141B VAL* 2.8 57.2 + - + +
143C GLU* 3.2 36.6 - - - +
162C LYS* 4.4 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.6 3.6 - - + -
100B PRO* 3.8 35.7 - - + +
101B VAL* 2.9 26.6 + - - +
102B SER* 3.9 15.5 - - - +
103B VAL* 4.1 22.4 - - + -
119B LYS* 1.3 75.7 - - - +
121B ASP* 1.3 61.5 + - - +
122B SER 3.3 28.5 - - - +
123B PHE* 4.2 4.7 - - + -
138B VAL* 4.2 12.6 - - + -
139B ASP 3.7 5.2 - - - +
140B ALA* 4.2 1.6 - - + -
201B OTP 4.5 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS* 2.8 33.2 + - - +
120B ILE* 1.3 75.1 - - - +
122B SER* 1.3 62.6 + - - +
139B ASP* 2.8 22.6 + - + +
141B VAL* 3.4 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 4.6 11.9 + - - -
28A LEU 5.3 1.4 + - - -
29A SER* 5.8 1.4 - - - -
30A VAL* 5.6 1.0 - - - +
120B ILE* 3.3 10.5 - - - +
121B ASP* 1.3 83.1 - - - +
123B PHE* 1.3 61.6 + - - +
137B GLY 4.4 0.2 - - - -
138B VAL* 3.2 21.1 - - - -
139B ASP* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 5.6 1.1 - - - -
44B LEU* 3.8 20.0 - - + -
46B ARG* 3.8 21.1 - - - -
99B LYS* 3.5 34.3 - - + +
100B PRO* 3.8 28.7 - - + +
120B ILE* 4.2 10.3 - - + -
122B SER* 1.3 78.6 - - - +
124B LYS* 1.3 63.5 + - - +
125B CYS* 3.3 34.8 - - - -
136B CYS* 4.0 2.9 - - + -
137B GLY 3.3 6.7 - - - -
138B VAL* 3.8 18.2 - - + -
201B OTP 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE 3.0 16.2 + - - -
26A GLY* 2.9 29.1 + - - +
27A GLY* 3.9 14.1 - - - +
28A LEU* 3.4 26.4 - - + +
99B LYS* 6.3 0.2 - - - +
123B PHE* 1.3 76.6 - - - +
125B CYS* 1.3 73.8 + - - +
126B MET* 3.9 24.6 - - - +
136B CYS* 3.3 2.1 - - - +
137B GLY 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.8 0.2 - - - -
46B ARG* 3.6 18.8 - - - +
123B PHE* 3.3 26.4 - - - -
124B LYS* 1.3 80.0 - - - +
126B MET* 1.3 66.2 + - - +
134B GLU* 3.6 17.7 - - - +
135B VAL 3.2 4.7 - - - +
136B CYS* 2.2 43.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.0 22.7 - - + +
28A LEU* 4.0 21.1 - - + -
124B LYS* 3.9 29.4 - - - +
125B CYS* 1.3 77.7 - - - +
127B PRO* 1.3 86.6 - - + +
128B HIS 3.3 0.2 + - - -
129B PRO* 4.2 18.4 - - + -
134B GLU* 3.6 6.6 - - - +
135B VAL* 2.9 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B MET* 1.3 98.9 - - + +
128B HIS* 1.3 67.3 + - - +
129B PRO* 3.2 9.5 - - - +
132B LYS* 3.7 19.1 - - + +
133B ARG 3.9 1.3 - - - +
134B GLU* 4.4 3.4 - - + -
----------------------------------------------------------
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