Contacts of the strand formed by residues 128 - 138 (chain D) in PDB entry 4WFH
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 GLY 128 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D GLN* 3.4 29.4 + - - +
124D LEU* 3.5 13.9 - - - +
126D SER* 3.3 5.8 + - - -
127D GLY* 1.3 80.5 - - - +
129D ALA* 1.3 63.9 + - - +
179D THR* 6.3 0.9 - - - -
180D LEU 4.0 5.2 - - - -
181D THR* 4.8 0.4 - - - -
182D LYS 4.3 0.9 - - - -
146E LYS* 6.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D PRO* 4.0 11.7 - - + -
123D GLN* 3.6 5.8 - - - +
124D LEU* 3.8 13.2 - - + -
128D GLY* 1.3 75.7 - - - +
130D SER* 1.3 62.8 + - - +
131D VAL* 4.0 1.9 + - - +
178D LEU 3.7 1.7 - - - +
179D THR* 5.0 1.2 - - - +
180D LEU* 2.8 42.9 + - - +
181D THR 4.3 0.4 - - - +
182D LYS* 4.2 4.3 - - - -
185D TYR* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D PHE 4.3 0.3 - - - +
118D PRO 4.3 1.2 - - - +
119D PRO* 3.6 21.0 - - - +
123D GLN* 3.0 30.9 + - - +
129D ALA* 1.3 71.3 - - - +
131D VAL* 1.3 62.5 + - - +
132D VAL* 4.0 5.2 + - - +
177D THR* 4.2 12.1 - - - +
178D LEU 3.3 6.3 - - - -
179D THR* 3.6 22.9 + - - +
127E LEU* 5.5 2.6 - - - +
144E LEU* 3.9 19.5 - - - +
146E LYS* 3.8 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ILE* 4.2 2.9 - - + -
117D PHE 3.3 16.8 - - - +
119D PRO* 4.0 17.0 - - + -
129D ALA 4.6 3.6 - - - +
130D SER* 1.3 77.0 - - - +
132D VAL* 1.3 60.5 + - - +
147D TRP* 3.5 29.8 - - + -
177D THR* 3.5 2.1 - - - -
178D LEU* 2.7 50.9 + - + +
180D LEU* 4.8 2.9 - - + -
185D TYR* 4.6 7.9 - - + -
191D TYR* 4.6 19.1 - - + -
208D PHE* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ILE* 3.4 4.3 - - - +
117D PHE* 2.8 45.5 + - + -
130D SER 4.4 6.7 - - - +
131D VAL* 1.3 79.2 - - - +
133D CYS* 1.3 64.5 + - - +
134D PHE* 3.4 36.6 - - + -
147D TRP* 4.0 1.3 - - - -
175D SER* 5.3 0.7 - - - -
176D SER 3.6 6.5 - - - +
177D THR* 4.0 22.4 - - + +
127E LEU* 4.1 26.9 - - + -
144E LEU* 4.5 15.5 - - + -
181E SER* 4.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D VAL* 3.8 17.3 - - - -
115D SER 3.1 14.8 - - - -
116D ILE* 4.4 1.6 - - - -
132D VAL* 1.3 75.7 - - - +
134D PHE* 1.3 63.2 + - - +
135D LEU* 3.8 9.2 - - + +
147D TRP* 3.7 14.4 - - + -
175D SER* 3.3 3.8 - - - -
176D SER* 2.8 40.2 + - - +
193D CYS* 2.0 50.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D THR 3.3 2.2 - - - +
114D VAL* 3.2 7.3 - - - +
115D SER* 2.9 37.5 + - - +
117D PHE* 3.7 23.8 - + - -
132D VAL* 3.4 17.5 - - + -
133D CYS* 1.3 79.7 - - - +
135D LEU* 1.3 60.9 + - - +
136D ASN* 3.7 16.4 - - - +
174D MET 3.7 2.2 - - - -
175D SER* 4.0 5.2 - - - -
127E LEU* 3.8 20.2 - - + -
140E THR* 4.0 7.4 - - + -
141E LEU 4.2 1.3 - - - -
142E GLY* 4.0 10.1 - - - -
169E PHE* 4.0 17.0 - + - -
181E SER* 3.9 17.5 - - - -
182E SER 4.0 11.2 - - - -
183E SER* 3.3 33.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D PRO* 4.2 10.3 - - + -
113D THR 3.6 3.6 - - - -
114D VAL* 4.3 9.4 - - + -
133D CYS* 3.8 25.8 - - + +
134D PHE* 1.3 77.7 - - - +
136D ASN* 1.3 58.6 - - - +
138D PHE* 3.2 14.7 - - + -
143D ILE* 3.6 17.0 - - + -
145D VAL* 3.3 36.1 - - + -
174D MET* 2.8 53.5 + - + +
176D SER 4.8 2.9 - - - +
193D CYS* 4.6 0.4 - - - -
195D ALA* 3.5 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D PRO* 3.8 0.9 - - - +
113D THR* 2.9 44.8 + - - +
134D PHE* 3.7 15.5 - - - +
135D LEU* 1.3 84.8 + - - +
137D ASN* 1.3 82.7 - - - +
138D PHE* 3.5 2.6 + - - -
173D SER* 3.7 2.6 - - - -
140E THR* 4.5 10.7 + - - +
167E HIS* 3.6 14.0 - - - -
169E PHE* 3.7 13.9 - - - -
183E SER* 3.2 29.3 + - - -
185E THR* 4.6 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ALA* 3.7 13.7 - - - +
111D ALA 3.8 5.4 - - - +
113D THR* 5.1 5.2 + - - +
136D ASN* 1.3 84.0 - - - +
138D PHE* 1.3 59.0 + - - +
169D ASP* 3.4 12.1 - - - +
171D THR* 3.1 30.5 + - + +
172D TYR 3.0 13.6 + - - -
173D SER* 3.0 3.1 + - - -
167E HIS* 3.1 36.0 + - - -
185E THR* 5.6 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ALA* 3.2 18.8 - - - +
112D PRO* 3.6 27.1 - - + -
135D LEU* 3.2 34.1 - - + -
136D ASN 4.1 0.2 - - - -
137D ASN* 1.3 75.1 - - - +
139D TYR* 1.3 62.5 + - - +
140D PRO 3.2 27.4 - - - -
141D LYS* 3.7 20.0 - - - -
143D ILE* 3.8 28.9 - - + -
162D TRP* 5.0 3.4 - + - -
171D THR* 3.6 1.4 - - - -
172D TYR* 2.8 54.6 + - + +
173D SER* 3.6 8.5 - - - -
174D MET* 3.9 7.0 - - + -
197D HIS* 3.6 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