Contacts of the strand formed by residues 136 - 143 (chain H) in PDB entry 1GN2
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 LYS 136 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ALA 2.9 39.2 + - - +
3F GLU* 4.0 6.9 - - - +
4F TYR* 3.8 36.8 - - + +
41F ASN* 4.7 0.8 + - - -
44F VAL* 4.4 19.5 - - + +
102H ALA* 6.4 0.2 - - + -
130H TRP* 3.5 9.8 - - - -
131H ASP* 2.7 36.9 + - - +
134H GLY 3.2 18.8 - - - +
135H ASN* 1.3 75.4 - - - +
137H LEU* 1.3 68.0 - - - +
138H LEU* 3.8 16.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H LEU* 4.9 5.6 - - + -
98H ALA* 4.7 8.5 - - + -
99H ILE* 3.9 37.7 - - + +
102H ALA* 4.0 22.6 - - + +
103H PHE* 3.9 17.9 - - + -
128H LEU* 4.1 17.3 - - + -
129H GLY 3.5 8.3 - - - +
130H TRP* 3.7 21.3 - - + -
136H LYS* 1.3 74.9 - - - +
138H LEU* 1.3 68.8 + - - +
156H LEU* 3.6 28.9 - - + -
194H TYR* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F TYR* 3.8 7.0 - - - +
44F VAL* 4.6 13.7 - - + -
47F LEU* 6.1 1.8 - - + -
66F LEU* 4.5 23.6 - - + -
70F LEU* 3.6 31.4 - - + -
103H PHE* 4.2 6.3 - - + -
128H LEU* 3.5 2.9 - - - +
129H GLY 2.7 39.7 + - - +
131H ASP* 3.8 20.0 - - + -
136H LYS* 4.2 14.1 - - + +
137H LEU* 1.3 83.0 - - - +
139H ILE* 1.3 65.8 - - - +
140H PHE* 4.0 21.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F GLU* 2.5 37.3 - - - +
66F LEU* 3.6 11.7 - - - +
103H PHE* 3.5 33.4 - - + -
109H PHE* 3.8 24.9 - - + +
112H GLN* 3.5 30.6 + - + +
113H PHE* 3.9 23.3 - - + +
116H ALA* 4.1 15.5 - - + -
127H ALA 3.3 9.2 - - - +
128H LEU* 4.3 6.1 - - + -
138H LEU* 1.3 75.7 - - - +
140H PHE* 1.3 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F GLU* 3.5 4.5 - - - -
66F LEU* 4.1 21.8 - - + -
67F ALA* 4.4 9.6 - - + -
70F LEU* 4.4 2.5 - - + -
151F LEU* 5.8 1.8 - - + -
116H ALA* 4.8 0.4 - - - +
126H ALA* 3.8 3.1 - - - -
127H ALA* 2.8 40.9 + - + +
129H GLY* 4.6 5.2 - - - -
138H LEU* 4.0 33.7 - - + -
139H ILE* 1.3 83.5 - - - +
141H GLN* 1.3 63.2 + - - +
142H VAL* 3.8 7.2 + - + -
148H ASN 4.3 12.1 - - - +
149H PHE* 4.1 18.2 - - + -
150H PRO* 3.5 23.8 - - + -
153H ILE* 3.6 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F ILE* 5.0 0.2 - - - +
60F LEU* 3.6 36.4 - - - +
63F GLU* 3.9 24.0 + - + +
116H ALA* 3.0 29.1 + - + +
119H THR* 2.7 41.4 + - - -
120H VAL* 3.7 14.6 - - + +
125H TRP 3.7 3.4 - - - +
126H ALA* 5.0 0.7 - - - +
140H PHE* 1.3 72.8 - - - +
142H VAL* 1.3 61.4 + - - +
143H TYR* 3.5 19.4 + - + -
148H ASN* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F LEU* 4.9 7.4 - - + -
75H ASN* 5.1 1.1 - - - +
120H VAL* 4.5 2.4 - - - +
124H GLY* 3.0 4.5 - - - -
125H TRP* 3.0 48.8 + - + +
127H ALA* 4.4 21.1 - - + -
140H PHE* 4.7 6.3 - - + +
141H GLN* 1.3 73.1 - - - +
143H TYR* 1.3 74.7 + - - +
144H ASP 4.2 2.9 - - - +
145H HIS* 3.8 26.0 - - - +
147H THR 3.3 11.7 - - - +
148H ASN* 4.4 0.2 - - - -
149H PHE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F LEU* 4.4 13.5 - - + +
64F LYS* 3.7 27.7 - - + +
64G LYS* 4.7 15.4 + - - -
120H VAL* 4.5 13.2 - - + -
121H GLN 5.6 1.8 - - - -
123H CYS 3.8 5.4 - - - +
141H GLN* 3.5 35.4 + - - -
142H VAL* 1.3 77.7 - - - +
144H ASP* 1.3 76.3 + - - +
145H HIS 2.9 4.7 + - - -
147H THR* 2.8 48.1 + - + -
148H ASN* 3.4 26.3 + - + -
----------------------------------------------------------
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