Contacts of the strand formed by residues 199 - 207 (chain A) in PDB entry 1HXD
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 ALA 199 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 3.4 4.3 - - - +
139A LEU* 2.9 33.6 + - + -
142A GLY* 3.2 29.8 - - - +
143A PRO* 3.3 11.9 - - + -
191A LEU* 4.6 5.8 - - + -
192A THR 3.2 9.6 - - - +
193A GLY* 4.4 0.9 - - - -
197A ASP 3.5 0.6 + - - -
198A ALA* 1.3 74.9 - - - +
200A GLN* 1.3 59.4 + - - +
201A ILE* 3.3 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 6.0 1.0 - - - +
98A ILE* 3.5 38.6 - - + +
136A PHE* 3.8 6.5 - - + -
137A TRP 3.8 2.9 - - - -
138A ARG* 2.9 47.5 + - - +
190A GLU 3.8 1.0 - - - +
191A LEU* 3.6 3.8 - - - -
192A THR* 2.8 41.9 + - - +
193A GLY* 5.5 0.2 - - - -
198A ALA* 3.9 11.2 + - - +
199A ALA* 1.3 74.8 - - - +
201A ILE* 1.4 58.8 + - - +
202A VAL* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A MET 3.4 1.2 - - - +
136A PHE* 3.2 7.4 - - - -
137A TRP* 2.6 48.8 + - + +
139A LEU* 3.8 26.5 - - + -
146A ALA* 5.6 5.8 - - + -
149A LEU* 4.3 13.9 - - + -
189A VAL* 3.6 19.1 - - + -
190A GLU 3.6 3.4 - - - +
191A LEU* 4.6 9.6 - - + -
199A ALA* 3.3 28.9 - - + +
200A GLN* 1.4 71.8 - - - +
202A VAL* 1.3 68.2 + - - +
203A ILE* 3.1 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 3.8 41.4 + - + +
94A LEU* 3.9 27.4 - - + -
95A LEU* 4.2 15.9 - - + +
98A ILE* 4.2 12.1 - - + -
134A SER* 4.6 0.2 - - - -
135A MET 3.6 1.3 - - - -
136A PHE* 3.5 22.9 - - + -
188A LEU 3.8 1.0 - - - +
189A VAL* 3.5 1.2 - - - -
190A GLU* 2.7 43.9 + - + +
201A ILE* 1.3 80.6 - - - +
203A ILE* 1.3 64.0 + - - +
204A GLY 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 3.6 2.2 - - - -
133A LEU 3.6 0.3 - - - +
134A SER* 2.8 12.6 - - - -
135A MET* 2.8 51.6 + - + +
137A TRP* 4.4 10.5 - - + -
149A LEU* 4.0 19.1 - - + -
153A ILE* 4.2 24.2 - - + -
187A ILE* 4.4 8.5 - - + -
188A LEU 3.7 0.9 - - - -
189A VAL* 3.7 25.4 - - + -
201A ILE* 3.1 33.2 - - + -
202A VAL* 1.3 74.0 - - - +
204A GLY* 1.3 57.8 + - - +
205A ALA* 4.2 1.3 + - + -
250A LEU* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 3.1 19.1 + - - -
133A LEU 3.1 5.4 - - - -
187A ILE* 3.2 8.8 - - - +
188A LEU 2.6 42.5 + - - -
203A ILE* 1.3 74.0 - - - +
205A ALA* 1.3 61.8 + - - -
500A BTN 3.5 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 3.8 4.3 - - - +
133A LEU* 2.8 45.7 + - + +
153A ILE* 5.5 3.6 - - + -
157A MET* 3.9 35.9 - - + -
185A ALA* 6.2 0.2 - - + -
186A GLY 3.4 4.9 - - - +
187A ILE* 4.7 5.2 - - + -
203A ILE* 4.2 1.3 + - + -
204A GLY* 1.3 77.0 - - - +
206A GLY* 1.3 59.1 + - - +
207A ILE* 4.9 4.8 - - + +
500A BTN 3.4 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 4.1 17.9 - - - -
131A LEU 3.6 4.7 - - - -
185A ALA* 2.8 7.3 - - - +
186A GLY 2.6 42.6 + - - -
205A ALA* 1.3 73.9 - - - +
207A ILE* 1.4 62.3 + - - -
500A BTN 3.5 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 4.9 1.0 - - - +
130A ASN* 3.1 25.1 - - - +
131A LEU* 2.9 48.1 + - + +
157A MET* 4.6 13.9 - - + -
161A LEU* 4.9 22.0 - - + -
184A LEU* 3.9 13.9 - - + +
185A ALA* 3.9 13.2 - - + -
205A ALA* 4.9 5.2 - - + -
206A GLY* 1.4 82.2 - - - +
208A ASN* 1.3 68.1 + - - +
209A MET* 3.2 10.4 + - + +
226A LEU* 4.9 6.1 - - + -
238A LEU* 4.5 8.3 - - + -
242A LEU* 4.4 9.0 - - + -
----------------------------------------------------------
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