Contacts of the helix formed by residues 107 - 120 (chain B) in PDB entry 3SFX
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 ASP 107 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ALA 4.0 1.2 + - - -
106B LEU* 1.3 76.2 - - - +
108B GLN* 1.3 64.3 + - - +
109B GLY* 3.6 4.8 + - - +
110B THR* 2.7 35.5 + - - -
111B LYS* 3.0 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 4.0 0.6 + - - -
107B ASP* 1.3 74.0 - - - +
109B GLY* 1.3 57.7 + - - +
111B LYS* 3.1 28.8 + - - +
112B ASP* 2.8 61.9 + - - +
153B ALA 4.9 0.2 - - - +
155B ASN* 3.8 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASP* 3.3 6.9 + - - -
108B GLN* 1.3 76.3 - - - +
110B THR* 1.3 61.1 + - - +
112B ASP* 3.4 10.8 + - - +
113B ARG* 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 5.4 0.2 - - + -
74B PHE* 3.8 32.1 - - + -
75B PHE* 4.3 15.7 - - + -
106B LEU* 4.0 17.5 - - + -
107B ASP* 2.7 29.7 + - - -
109B GLY* 1.3 72.8 - - - +
111B LYS* 1.3 65.7 + - - +
113B ARG* 3.2 16.5 + - - +
114B VAL* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ALA* 6.3 0.2 - - - -
106B LEU* 3.8 37.6 + - + +
107B ASP 3.0 14.5 + - - +
108B GLN* 3.1 33.4 + - - +
110B THR* 1.3 75.1 - - - +
112B ASP* 1.3 58.3 + - - +
114B VAL* 3.2 11.5 + - - +
115B VAL* 3.0 31.8 + - - +
152B ILE 4.7 9.8 + - - -
153B ALA* 3.4 27.4 + - - +
154B GLY 5.6 2.2 + - - +
155B ASN* 6.1 0.2 - - - +
507B ARG* 4.5 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLN* 2.8 47.3 + - - +
109B GLY* 3.6 10.0 - - - +
111B LYS* 1.3 73.6 - - - +
113B ARG* 1.3 60.0 + - + +
115B VAL* 3.8 7.4 - - - +
116B SER* 2.9 31.2 + - - -
155B ASN* 4.8 4.0 + - - -
159B THR* 4.5 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PRO 5.4 2.0 - - - +
28A ASN* 2.8 37.8 + - + +
29A PRO 3.1 26.5 + - - -
30A VAL* 3.9 15.0 - - + +
75B PHE* 3.3 48.3 + - - +
109B GLY 3.2 19.5 + - - +
110B THR* 3.2 17.4 + - - +
112B ASP* 1.3 72.5 - - + +
114B VAL* 1.3 57.7 + - - +
116B SER* 4.0 5.5 - - - -
117B THR* 2.7 39.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.0 22.8 - - + +
74B PHE* 4.1 20.0 - - + -
92B VAL* 3.8 26.9 - - + -
96B VAL* 4.4 10.5 - - + -
106B LEU* 4.5 5.4 - - + -
110B THR 3.1 16.3 + - - +
111B LYS* 3.4 7.4 - - - +
113B ARG* 1.3 76.6 - - - +
115B VAL* 1.3 63.8 + - + +
117B THR* 3.4 1.4 + - - -
118B LEU* 3.1 37.7 + - + +
149B SER 4.7 1.1 - - - +
153B ALA* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LYS 3.0 19.0 + - - +
112B ASP* 3.8 7.2 - - - +
114B VAL* 1.3 75.3 - - + +
116B SER* 1.3 59.5 + - - +
118B LEU* 3.2 4.0 + - - +
119B LEU* 2.9 39.6 + - + +
150B LEU* 4.0 16.1 - - + +
153B ALA* 3.9 7.0 - - + +
154B GLY* 3.8 30.1 - - - +
155B ASN* 6.0 0.7 - - - +
159B THR 3.7 17.3 - - - +
160B GLY* 3.8 4.3 - - - +
161B GLY* 3.7 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP 5.1 0.5 + - - -
27A PRO* 4.1 20.0 + - - +
112B ASP 2.9 18.5 + - - -
113B ARG* 4.0 5.6 - - - -
115B VAL* 1.3 77.5 - - - +
117B THR* 1.3 59.8 + - - +
119B LEU* 3.3 8.9 + - - +
120B HIS* 2.7 49.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
25A ASP 4.3 9.6 - - - +
27A PRO 5.4 0.3 + - - -
29A PRO* 3.3 15.4 - - + +
30A VAL* 2.9 47.6 + - + +
31A VAL* 5.3 0.2 - - + -
88B ARG* 4.3 0.4 - - - +
92B VAL* 5.2 3.1 - - + -
113B ARG 2.7 23.7 + - - -
114B VAL 3.6 4.0 - - - -
116B SER* 1.3 75.1 - - - +
118B LEU* 1.3 64.6 + - - +
120B HIS* 3.2 13.3 + - - +
121B PHE* 3.4 39.3 - - + -
----------------------------------------------------------
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 PRO* 4.4 4.3 - - + -
92B VAL* 4.1 28.0 - - + -
114B VAL* 3.1 32.3 + - + +
115B VAL 3.7 3.4 - - - +
117B THR* 1.3 74.0 - - - +
119B LEU* 1.3 61.6 + - - +
121B PHE* 3.0 34.6 + - + +
128B PHE* 3.3 23.7 - - + -
146B SER* 3.9 30.7 - - - +
149B SER* 3.5 28.0 - - - -
150B LEU* 4.0 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 2.9 39.5 + - + +
116B SER* 3.9 8.3 - - - +
117B THR 3.3 0.4 - - - -
118B LEU* 1.3 76.1 - - - +
120B HIS* 1.3 62.7 + - + +
121B PHE 3.1 0.2 - - - -
122B LEU* 3.2 35.0 + - + +
128B PHE* 4.9 2.5 - - + -
150B LEU* 4.6 15.9 - - + -
159B THR 6.2 0.4 - - - -
161B GLY* 4.1 7.9 - - - +
164B ASP* 3.7 47.8 - - + +
165B LEU* 5.3 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.7 32.0 + - - +
25A ASP* 3.6 12.9 + - - +
26A GLY* 3.3 34.1 - - - -
27A PRO* 4.3 4.6 - - + +
116B SER* 2.7 36.8 + - - -
117B THR 3.2 10.2 + - - +
118B LEU 3.2 0.8 - - - -
119B LEU* 1.3 78.4 - - + +
121B PHE* 1.3 60.9 + - + +
122B LEU 3.3 1.3 + - - -
132B PRO* 3.4 2.9 - - - +
133B ALA* 2.9 24.9 + - - +
----------------------------------------------------------
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