Contacts of the strand formed by residues 97 - 104 (chain G) in PDB entry 6ALG
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 97 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G LYS* 3.6 16.2 - - - +
96G ASP* 1.3 80.1 - - + +
98G VAL* 1.3 67.0 + - - +
99G ILE* 6.0 5.2 - - + +
145G LYS* 3.3 30.6 + - - -
146G VAL 3.4 5.4 - - - +
147G GLN* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G VAL* 4.1 10.5 - - + -
95G LYS* 3.6 32.3 - - + +
96G ASP 5.4 0.9 - - - +
97G GLU* 1.3 80.4 - - - +
99G ILE* 1.3 69.1 + - - +
100G LEU* 3.7 21.3 - - + -
118G ASP* 5.1 5.4 - - - +
121G VAL* 3.7 23.8 - - + -
144G ILE 3.7 0.3 - - - +
145G LYS* 3.4 4.9 - - - +
146G VAL* 2.9 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G GLU* 6.0 5.2 - - - +
98G VAL* 1.3 81.2 - - - +
100G LEU* 1.3 73.2 + - - +
101G THR* 4.5 4.5 + - - +
118G ASP* 4.3 10.4 - - - +
143G ARG* 4.3 23.8 - - + -
144G ILE 3.3 6.1 - - - +
145G LYS* 4.4 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LEU* 5.1 2.2 - - + -
90G VAL* 4.8 1.6 - - + -
98G VAL* 3.7 32.5 - - + -
99G ILE* 1.3 75.9 - - - +
101G THR* 1.3 68.4 + - - +
115G ILE* 3.6 28.7 - - + -
116G THR 4.7 4.9 - - - +
118G ASP* 5.0 7.9 - - - +
121G VAL* 3.7 28.5 - - + -
123G ILE* 4.6 13.7 - - + -
143G ARG* 3.4 3.5 - - - -
144G ILE* 2.5 50.8 + - + +
146G VAL* 4.2 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G ILE* 4.5 6.2 + - - +
100G LEU* 1.3 80.1 + - - +
102G LEU* 1.3 63.1 + - - +
103G ASN* 3.4 29.4 + - - +
115G ILE* 4.6 3.7 - - - +
116G THR* 2.9 44.7 + - - +
118G ASP* 5.7 0.2 + - - -
141G SER 6.0 0.2 - - - -
142G MET 3.6 11.9 - - - +
143G ARG* 4.2 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G THR* 1.3 71.8 - - - +
103G ASN* 1.3 73.1 + - - +
104G LYS* 4.5 6.1 - - + -
110G VAL* 3.7 24.5 - - + -
111G THR 4.7 1.6 - - - +
114G ASP 3.9 13.7 - - - +
115G ILE* 3.7 26.9 - - + -
130G ILE* 4.4 17.3 - - + -
140G ILE* 3.7 33.4 - - + -
141G SER* 3.4 2.8 - - - -
142G MET* 3.1 43.7 + - + +
144G ILE* 4.6 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G THR* 3.4 26.6 + - - +
102G LEU* 1.3 80.9 - - - +
104G LYS* 1.3 63.9 + - - +
114G ASP* 3.9 10.4 + - - +
116G THR* 5.4 2.4 + - - -
139G SER* 5.6 0.7 - - - +
140G ILE 4.1 3.1 - - - -
141G SER* 3.3 22.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LEU* 4.5 3.3 - - + +
103G ASN* 1.3 76.3 - - - +
105G SER* 1.3 74.1 + - - +
106G GLY 5.2 1.8 + - - -
108G GLY* 5.3 3.6 - - - -
109G PRO 3.2 19.6 + - - -
110G VAL* 3.8 26.9 - - + +
114G ASP* 3.0 45.6 + - + +
133G LEU* 3.4 11.3 - - + +
139G SER* 2.5 26.6 + - - -
140G ILE* 3.7 10.7 + - + +
----------------------------------------------------------
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