Contacts of the strand formed by residues 152 - 159 (chain H) in PDB entry 1P7G
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 GLN 152 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E THR* 3.7 11.4 - - - +
16E LYS* 2.9 51.9 + - + +
18E TYR* 3.2 28.4 + - - +
58E LEU* 3.9 4.9 - - - +
65E ARG* 5.5 0.7 + - - -
118H PHE* 3.4 28.8 - - + +
146H TYR* 3.6 10.0 - - - -
147H GLU* 2.8 30.1 + - + +
150H GLU* 4.2 1.9 - - - +
151H GLU* 1.3 73.5 - - - +
153H LEU* 1.3 68.0 + - - +
154H LEU* 4.1 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ARG* 4.9 2.4 + - - -
111H ILE* 4.4 7.6 - - + -
114H LEU* 3.7 27.8 - - + -
115H ILE* 3.9 29.4 - - + +
118H PHE* 3.7 23.3 - - + +
119H PHE* 4.1 17.4 - - + -
144H LEU* 4.0 13.9 - - + -
145H VAL 3.2 6.1 - - - +
146H TYR* 4.1 4.3 - - + -
152H GLN* 1.3 79.5 - - - +
154H LEU* 1.3 70.8 + - - +
172H LEU* 3.2 34.8 - - + -
210H LEU* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E TYR* 4.1 8.5 - - - +
58E LEU* 3.7 27.6 - - + -
61E LEU* 5.3 0.2 - - + -
65E ARG* 4.5 11.4 - - - +
80E LEU* 4.3 17.9 - - + -
84E LEU* 3.8 28.9 - - + -
119H PHE* 4.9 2.7 - - - -
144H LEU* 3.5 3.9 - - - +
145H VAL* 2.8 44.1 + - + +
147H GLU* 3.9 18.8 - - + -
152H GLN* 4.1 14.1 - - + +
153H LEU* 1.3 84.0 - - - +
155H ILE* 1.3 67.3 + - - +
156H LEU* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E LEU* 5.6 0.7 - - - +
65E ARG* 5.0 0.8 - - - +
77E LEU* 3.2 19.2 - - + +
80E LEU* 4.5 1.7 - - - +
119H PHE* 3.8 20.8 - - + -
125H PHE* 3.9 8.1 - - + -
128H GLU* 3.6 31.1 + - + +
129H PHE* 3.6 46.2 - - + +
132H ALA* 3.9 27.8 - - + -
142H ALA 5.6 0.4 - - - -
143H ILE 3.2 11.4 - - - +
144H LEU* 4.1 10.3 - - + -
154H LEU* 1.3 78.7 - - - +
156H LEU* 1.3 74.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E LEU* 4.1 10.5 - - + +
80E LEU* 4.0 25.1 - - + -
81E SER* 4.7 15.5 - - - +
84E LEU* 5.1 2.5 - - + -
132H ALA* 5.2 0.3 - - - +
142H ALA* 3.6 4.3 - - - -
143H ILE* 2.9 48.1 + - + +
145H VAL* 4.2 19.5 - - + -
154H LEU* 4.6 7.4 - - + -
155H ILE* 1.3 86.9 - - - +
157H GLN* 1.3 64.3 + - - +
158H ILE* 4.5 3.1 - - + -
164H MSE 3.9 9.6 - - - +
165H HIS 4.4 0.2 - - - -
166H ALA* 3.7 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ILE* 4.0 1.7 - - - +
74E ARG* 3.0 53.4 + - - +
77E LEU* 3.5 29.0 + - + +
78E ARG* 4.8 0.6 - - - +
81E SER* 5.4 0.2 - - - -
132H ALA* 3.0 30.6 - - + +
135H ASN* 3.1 16.4 + - - +
136H VAL* 4.2 12.2 - - + +
137H GLU 5.0 0.4 - - - +
141H TRP 3.7 3.8 - - - -
142H ALA* 5.0 0.4 - - - +
156H LEU* 1.3 74.5 - - - +
158H ILE* 1.3 63.2 + - - +
159H GLU* 5.3 1.4 + - - +
164H MSE 3.1 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H VAL* 4.1 5.6 - - - +
140H GLY* 3.1 3.1 - - - -
141H TRP* 2.8 47.7 + - + +
143H ILE* 3.7 31.0 - - + -
156H LEU* 4.5 2.9 - - + -
157H GLN* 1.3 81.5 - - - +
159H GLU* 1.3 61.1 + - - +
160H LYS 4.4 0.7 - - - +
161H HIS* 3.6 36.3 - - - +
163H LEU 3.1 15.0 - - - +
164H MSE 3.7 5.2 - - - +
165H HIS* 3.4 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ARG* 5.1 0.7 - - - -
78E ARG* 2.7 37.0 + - - -
160F LYS* 3.2 26.5 + - - +
163F LEU* 5.6 0.9 - - - +
136H VAL* 4.8 5.2 - - + -
137H GLU* 3.7 25.2 + - - +
139H VAL 3.7 3.6 - - - +
157H GLN* 5.3 1.9 + - - +
158H ILE* 1.3 72.7 - - - +
160H LYS* 1.3 76.3 + - + +
163H LEU* 3.0 49.3 + - + +
164H MSE 3.6 18.8 - - + +
----------------------------------------------------------
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