Contacts of the strand formed by residues 127 - 134 (chain G) in PDB entry 1H4O
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 ARG 127 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G GLY 3.4 7.0 - - - +
39G VAL* 4.0 0.8 - - - +
40G PRO* 3.7 14.4 - - + +
46G GLY* 4.4 0.2 - - - -
47G CYS* 3.3 25.1 - - - +
51G HIS* 3.0 47.7 + - + +
125G LEU 3.7 1.8 + - - -
126G LYS* 1.3 70.3 - - - +
128G PHE* 1.3 59.2 + - - +
142G VAL* 3.8 2.9 - - - +
143G GLU* 3.0 32.1 + - + +
146G GLY 2.8 17.7 + - - +
147G THR 3.0 17.1 + - - -
148G GLY 2.8 25.8 + - - -
149G LEU* 3.5 17.9 - - - +
152G SER* 3.1 15.7 - - - +
1162G BEZ 3.0 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.7 26.2 - - + -
37G PHE* 3.2 9.7 - - - +
38G GLY* 2.8 49.1 + - - +
51G HIS* 3.9 2.1 - - - -
73G LEU* 4.6 2.9 - - + -
104G PHE* 3.7 24.2 - + - -
110G LEU* 3.9 22.9 - - + -
125G LEU* 4.3 11.2 - - + -
126G LYS 3.5 17.7 - - - +
127G ARG* 1.3 75.6 - - - +
129G SER* 1.3 70.5 + - - +
130G MET* 3.9 21.5 - - + -
140G LEU* 4.7 2.7 - - + -
141G ASN 3.1 14.4 - - - +
142G VAL* 4.2 16.6 - - + -
152G SER* 3.8 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G VAL* 5.2 0.7 - - - -
36G LEU 3.4 5.8 - - - -
37G PHE* 4.0 9.0 - - - -
55G PHE* 4.5 1.8 - - - -
128G PHE* 1.3 74.7 - - - +
130G MET* 1.3 68.1 + - - +
140G LEU* 3.6 1.2 - - - +
141G ASN* 2.8 56.4 + - - +
152G SER* 3.4 28.6 + - - -
157G ILE* 3.5 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ILE* 4.8 8.1 - - - -
9G ILE* 3.3 27.4 - - + -
35G VAL* 3.2 10.2 - - - +
36G LEU* 2.7 46.8 + - + +
104G PHE* 4.9 2.9 - - - -
110G LEU* 5.7 0.9 - - - -
128G PHE* 3.9 16.6 - - + -
129G SER* 1.3 80.8 - - - +
131G VAL* 1.3 63.9 + - - +
132G VAL* 3.2 26.6 + - + -
137G VAL* 4.0 13.5 - - + -
139G ALA 3.2 11.2 - - - +
140G LEU* 3.7 22.7 - - + -
157G ILE* 4.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LYS* 4.6 11.2 - - + -
34G GLY 3.6 8.3 - - - +
35G VAL* 4.7 2.5 - - + +
130G MET* 1.3 73.1 - - - +
132G VAL* 1.3 69.3 + - - +
133G GLN* 5.5 2.2 - - + +
137G VAL* 3.6 2.3 - - - -
138G LYS* 2.8 38.9 + - + -
139G ALA* 3.1 28.1 + - + +
157G ILE* 3.7 23.8 - - + -
160G GLN* 4.7 9.2 - - + +
161G LEU* 3.9 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G ILE* 3.8 14.4 - - + -
29G PHE* 3.7 31.0 - - + -
32G LYS 3.7 1.6 - - - +
33G LYS* 3.4 2.8 - - - +
34G GLY 2.7 39.5 + - - +
36G LEU* 4.5 1.8 - - + -
130G MET* 3.2 38.4 - - + +
131G VAL* 1.3 79.1 - - - +
133G GLN* 1.3 63.0 + - - +
135G GLY* 3.5 35.0 - - - +
136G ILE 3.3 4.7 - - - +
137G VAL* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F ASP* 2.8 37.8 + - + +
148F GLY* 4.9 6.9 - - - -
150F THR* 5.7 6.3 - - - +
32G LYS 3.8 0.9 - - - -
33G LYS* 4.1 22.7 - - + +
131G VAL* 4.2 2.2 - - + +
132G VAL* 1.3 72.1 - - - +
134G ASP* 1.3 73.5 + - + +
136G ILE* 2.8 29.4 + - - +
138G LYS* 3.7 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F PRO* 4.2 27.4 - - + +
145F ASP* 5.1 1.8 - - + +
29G PHE 3.6 11.7 - - - -
30G LYS* 4.2 9.7 + - - +
31G GLY* 3.5 24.2 + - - +
32G LYS 2.8 16.6 + - - +
132G VAL 4.1 0.2 - - - -
133G GLN* 1.3 74.3 - - + +
135G GLY* 1.3 55.5 + - - +
136G ILE* 3.5 9.4 + - + +
----------------------------------------------------------
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