Contacts of the helix formed by residues 106 - 121 (chain A) in PDB entry 1XGS
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 GLU 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 1.3 84.4 - - - +
107A LEU* 1.3 59.6 + - - +
109A GLU* 3.3 14.6 + - - +
110A ALA* 2.9 24.6 + - - +
142A ARG* 4.4 5.3 - - + +
144A PHE* 3.4 26.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 4.4 8.1 - - + -
105A ASP* 3.3 13.5 + - - +
106A GLU* 1.3 77.5 - - - +
108A MET* 1.3 62.1 + - - +
110A ALA* 3.3 11.6 + - - +
111A ALA* 3.3 10.2 + - - +
144A PHE* 3.5 41.7 - - + -
190A ALA* 4.0 6.8 - - + +
191A THR* 4.0 24.7 - - - +
192A ILE* 4.0 8.3 - - + -
275A ILE* 3.7 41.7 - - + +
277A ALA* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 4.0 20.6 - - + -
97A THR* 3.4 47.3 - - + +
98A VAL* 4.1 0.7 - - - -
99A ARG* 3.9 21.1 - - - +
104A GLU* 3.7 26.9 - - + +
105A ASP* 3.2 31.6 + - - +
107A LEU* 1.3 75.6 - - - +
109A GLU* 1.3 61.3 + - - +
111A ALA 3.4 1.4 + - - -
112A LYS* 3.0 20.0 + - - +
277A ALA* 4.1 9.2 - - + -
279A PHE* 3.2 20.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 3.6 21.1 + - - +
105A ASP 2.9 17.9 + - - +
106A GLU* 3.6 12.0 - - - +
108A MET* 1.3 74.1 - - - +
110A ALA* 1.3 60.1 + - - +
112A LYS* 3.7 7.0 - - + +
113A GLU* 2.8 41.3 + - + +
142A ARG* 3.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU 2.9 17.0 + - - +
107A LEU 3.5 6.3 - - - +
108A MET 3.3 0.2 - - - -
109A GLU* 1.3 76.8 - - - +
111A ALA* 1.3 57.6 + - - +
113A GLU* 3.7 1.2 - - - +
114A ALA* 2.8 32.0 + - - +
138A GLU* 4.2 7.6 - - - +
139A ILE* 4.2 12.0 - - + +
142A ARG* 3.6 27.8 - - + +
144A PHE* 3.7 18.4 - - + -
190A ALA* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU 3.3 9.3 + - - +
108A MET 3.7 3.8 - - - +
110A ALA* 1.3 80.5 - - - +
112A LYS* 1.3 61.5 + - - +
114A ALA* 3.3 5.2 + - - -
115A LEU* 3.1 18.0 + - - +
139A ILE* 4.7 0.4 - - - -
188A PRO* 3.3 26.3 - - - +
190A ALA* 4.2 12.0 - - + +
277A ALA* 4.0 24.5 - - + +
279A PHE* 3.7 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 3.4 26.0 + - - +
108A MET 3.0 16.6 + - - +
109A GLU* 3.7 6.1 - - + +
111A ALA* 1.3 74.6 - - - +
113A GLU* 1.3 69.4 - - - +
115A LEU* 3.2 7.1 + - + +
116A ASN* 3.0 39.8 + - - +
279A PHE* 3.5 42.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 2.8 33.5 + - + +
110A ALA 3.9 0.2 - - - +
112A LYS* 1.3 78.8 - - - +
114A ALA* 1.3 61.1 + - - +
116A ASN* 3.3 23.1 + - - +
117A ALA* 2.9 31.0 + - - +
138A GLU* 3.9 8.1 - - - +
142A ARG* 3.3 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 2.8 17.7 + - - +
111A ALA 3.4 6.7 - - - +
113A GLU* 1.3 76.6 - - - +
115A LEU* 1.3 62.2 + - - +
117A ALA* 3.3 3.6 + - - +
118A ALA* 3.1 22.9 + - - +
135A ILE* 3.8 20.1 - - + +
138A GLU* 3.7 12.7 - - + +
139A ILE* 3.8 22.9 - - + -
188A PRO* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA 3.1 12.7 + - - +
112A LYS* 3.4 10.3 - - + +
113A GLU 3.1 0.2 - - - -
114A ALA* 1.3 79.1 - - - +
116A ASN* 1.3 66.7 + - - +
118A ALA* 3.2 4.3 + - - +
119A ILE* 3.1 43.9 + - + +
186A ILE* 3.4 41.1 - - + +
188A PRO* 3.7 12.5 - - + +
279A PHE* 3.8 12.1 - - + -
280A GLU* 3.7 22.4 - - - +
281A HIS* 3.7 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 3.0 26.1 + - - +
113A GLU* 3.3 32.1 + - - +
115A LEU* 1.3 84.3 - - - +
117A ALA* 1.3 57.3 + - - +
119A ILE* 3.5 10.5 + - - +
120A SER* 3.1 30.0 + - - -
281A HIS* 5.5 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU 2.9 16.5 + - - +
114A ALA 3.5 5.6 - - - +
115A LEU 3.1 0.2 - - - -
116A ASN* 1.3 75.2 - - - +
118A ALA* 1.3 63.4 + - - +
120A SER* 2.9 20.9 + - - -
121A VAL* 3.4 15.8 + - - +
134A ALA* 4.1 15.9 - - + +
138A GLU* 3.7 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA 3.1 12.9 + - - +
115A LEU 3.7 6.7 - - - +
117A ALA* 1.3 76.3 - - - +
119A ILE* 1.3 63.1 + - - +
121A VAL* 3.1 24.2 - - - +
122A ALA* 3.1 4.0 + - - +
131A LEU* 3.1 19.8 - - + +
134A ALA* 4.2 5.1 - - - +
135A ILE* 3.7 15.9 - - + -
186A ILE* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.1 39.2 + - + +
116A ASN* 3.8 10.1 - - - +
118A ALA* 1.3 76.8 - - - +
120A SER* 1.3 63.1 + - - +
121A VAL 3.1 1.2 + - - -
122A ALA* 3.2 23.2 + - - +
186A ILE* 4.0 17.5 - - + -
281A HIS* 4.1 23.3 - - + -
283A ILE* 4.3 5.2 - - + -
290A VAL* 4.0 14.1 - - + +
292A VAL* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN 3.1 14.9 + - - -
117A ALA* 2.9 22.5 + - - -
118A ALA 3.3 0.2 - - - -
119A ILE* 1.3 77.7 - - - +
121A VAL* 1.3 62.8 + - - +
122A ALA 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA 3.4 14.8 + - - +
118A ALA* 3.1 16.8 - - - +
120A SER* 1.3 84.4 - - - +
122A ALA* 1.3 61.9 + - - +
123A ARG* 3.6 8.1 + - - +
126A VAL* 3.7 18.7 - - + +
130A GLU* 4.3 20.6 - - + +
131A LEU* 3.2 19.1 - - + -
134A ALA* 4.5 8.1 - - + -
----------------------------------------------------------
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