Contacts of the strand formed by residues 112 - 122 (chain A) in PDB entry 1G13
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 GLY 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 3.2 4.8 - - - -
41A THR 3.0 31.3 + - - +
110A LYS 3.5 2.1 + - - -
111A GLU* 1.3 75.5 - - - +
113A THR* 1.3 63.1 + - - -
114A TYR* 3.9 10.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.3 21.4 + - - +
38A MSE 3.5 36.6 - - + -
39A GLY 3.4 5.8 - - - +
40A SER* 3.7 3.5 - - - -
112A GLY* 1.3 74.0 - - - -
114A TYR* 1.3 71.1 + - - +
115A SER* 4.2 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL 4.0 1.1 - - - +
38A MSE 3.2 5.4 - - - +
39A GLY* 2.8 37.5 + - - +
40A SER* 4.9 2.5 - - - -
41A THR* 4.4 9.9 - - + -
45A LEU* 6.2 0.4 - - + -
103A LEU* 4.1 15.3 - - + -
104A PRO* 3.5 39.4 - - + +
109A PHE* 3.7 11.2 - + + -
110A LYS* 2.5 50.2 + - + +
111A GLU 5.5 0.2 - - - -
112A GLY* 3.9 18.4 - - - -
113A THR* 1.3 79.4 - - - +
115A SER* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL 3.6 3.1 - - - -
38A MSE 3.1 23.8 - - - +
101A TYR* 4.2 6.6 - - - +
103A LEU* 3.7 21.2 - - - +
113A THR* 4.2 6.5 + - - +
114A TYR* 1.3 72.1 - - - +
116A LEU* 1.3 60.3 + - - +
117A PRO* 3.8 7.9 - - - +
71B TYR* 4.6 7.5 + - - -
86B MSE 4.3 19.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.2 21.8 - - + +
36A SER* 3.2 3.1 - - - -
37A VAL* 2.8 47.2 + - + +
97A PRO* 3.8 11.7 - - + -
98A LEU* 5.2 5.8 - - + -
101A TYR* 3.6 19.5 - - + -
103A LEU* 3.7 20.0 - - + -
115A SER* 1.3 74.7 - - - +
117A PRO* 1.3 67.9 - - - +
119A SER* 3.5 21.3 - - - +
121A PHE* 4.2 24.9 - - + -
86B MSE 3.5 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 3.9 0.2 - - - -
101A TYR* 3.5 44.4 - - + +
115A SER* 3.8 4.7 - - - +
116A LEU* 1.3 91.7 - - - +
118A LYS* 1.3 69.4 + - - +
119A SER* 2.9 15.1 + - - -
71B TYR* 3.9 9.6 - - - +
79B HIS 5.1 0.7 - - - +
82B ASP* 3.2 13.5 - - + +
83B VAL* 3.7 30.5 - - + +
86B MSE 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 4.0 18.3 - - - +
23A GLU* 3.0 36.1 + - - +
34A THR* 3.6 15.7 - - + -
35A LEU 3.3 7.9 - - - -
36A SER* 3.3 11.9 - - - -
101A TYR* 4.7 4.2 + - - -
117A PRO* 1.3 72.5 - - - +
119A SER* 1.3 60.1 + - - +
78B GLU* 4.2 3.1 - - - +
79B HIS* 3.4 43.5 + - + +
82B ASP* 2.7 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.4 4.9 - - - +
35A LEU 2.9 29.0 + - - -
97A PRO* 3.8 27.8 - - - +
101A TYR* 3.8 7.1 - - - -
116A LEU* 3.5 12.8 - - - +
117A PRO 2.9 18.0 + - - -
118A LYS* 1.3 75.2 + - - +
120A GLU* 1.3 64.8 - - - +
121A PHE* 3.5 15.3 - - - -
78B GLU* 3.3 11.1 + - - -
79B HIS* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 4.3 22.7 - - + +
33A VAL 3.5 4.3 - - - +
34A THR* 2.7 26.1 + - - -
97A PRO* 5.5 2.3 - - - +
119A SER* 1.3 73.5 - - - +
121A PHE* 1.3 68.6 + - - +
78B GLU* 3.0 31.3 + - + +
79B HIS* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 3.3 5.6 - - - -
33A VAL* 2.9 44.2 + - + +
35A LEU* 3.9 32.1 - - + -
96A GLU 5.0 0.9 - - - -
97A PRO* 3.6 38.1 - - + -
98A LEU* 6.4 0.4 - - + -
116A LEU* 4.2 10.5 - - + -
119A SER* 3.5 28.3 - - - -
120A GLU* 1.3 75.8 - - - +
122A VAL* 1.3 65.4 + - - +
123A VAL 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 4.1 3.4 - - - +
32A ASN* 3.2 23.6 - - - +
33A VAL* 5.4 0.2 - - - -
121A PHE* 1.3 76.3 - - - +
123A VAL* 1.3 75.0 + - - +
124A PRO* 3.4 5.9 - - - +
125A ASP* 6.3 0.9 - - + -
----------------------------------------------------------
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