Contacts of the strand formed by residues 135 - 145 (chain H) in PDB entry 1YEE
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 SER 135 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H THR* 3.0 38.7 - - - +
132H THR 3.1 15.5 + - - +
133H GLY 3.1 1.8 + - - -
134H SER* 1.3 83.7 - - - +
136H VAL* 1.3 59.8 + - - +
190H THR* 4.0 16.4 - - - +
191H VAL 3.4 14.1 - - - -
192H THR* 4.5 2.7 - - - -
193H SER* 4.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H PRO* 4.0 27.4 - - + -
130H ASP* 3.4 13.2 - - + +
132H THR* 4.6 7.6 - - - +
135H SER* 1.3 76.0 - - - +
137H THR* 1.3 66.6 + - - +
138H LEU* 4.1 11.2 - - + -
189H VAL 3.8 0.3 - - - +
190H THR* 3.2 3.5 - - - +
191H VAL* 2.8 55.5 + - + +
192H THR 4.1 8.5 - - - +
193H SER* 4.6 2.7 - - - +
197H TRP* 4.3 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 137 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H PRO* 4.1 5.5 - - - +
130H ASP* 3.0 9.8 + - - +
131H THR* 3.3 23.3 - - - +
136H VAL* 1.3 76.8 - - - +
138H LEU* 1.3 72.6 + - - +
188H SER* 4.3 9.7 - - - -
189H VAL 3.2 4.7 - - - -
190H THR* 3.3 29.8 - - + +
114L THR* 5.6 3.8 - - + -
116L SER* 3.8 19.9 + - - +
118L PHE* 3.4 24.8 - - - -
135L PHE* 4.5 1.6 - - - -
137L ASN* 5.0 6.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
124H LEU 3.5 6.7 - - - +
126H PRO* 3.5 28.5 - - + -
136H VAL* 4.1 6.7 - - + -
137H THR* 1.3 78.2 - - - +
139H GLY* 1.3 59.7 + - - +
155H TRP* 4.8 0.2 - - + -
188H SER* 3.2 6.9 - - - -
189H VAL* 2.8 47.8 + - + +
191H VAL* 4.3 9.4 - - + -
197H TRP* 4.0 30.5 - - + -
203H ILE* 3.9 31.4 - - + -
221H ILE* 3.8 25.6 - - + -
118L PHE* 4.3 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 2.7 53.9 + - - +
138H LEU* 1.3 77.2 - - - +
140H CYS* 1.3 58.7 + - - -
155H TRP* 3.6 6.5 - - - -
187H SER 3.2 11.0 - - - -
221H ILE* 3.5 11.1 - - - +
135L PHE* 4.1 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 3.8 22.4 - - - -
122H TYR 3.5 7.0 - - - -
124H LEU* 3.6 3.7 - - - +
139H GLY* 1.3 75.5 - - - +
141H LEU* 1.3 60.9 + - - +
142H VAL* 4.9 1.6 - - - -
152H LEU* 4.2 10.2 - - + +
155H TRP* 3.7 12.6 - - + -
186H SER* 3.2 6.8 - - - -
187H SER* 3.0 27.2 + - - +
206H CYS* 2.0 50.9 - - - -
208H VAL* 4.5 0.2 - - - -
219H LYS* 5.2 1.8 - - - -
221H ILE* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H SER 3.6 1.4 - - - +
121H VAL* 3.4 4.5 - - - +
122H TYR* 2.8 57.6 + - + +
124H LEU* 4.1 16.2 - - + +
140H CYS* 1.3 72.3 - - - +
142H VAL* 1.3 61.1 + - - +
143H LYS* 4.2 13.7 - - + -
184H THR* 3.8 28.9 - - + -
185H LEU 3.8 5.6 - - - +
186H SER* 4.3 10.8 - - - +
124L GLN* 4.6 2.7 - - - +
131L SER* 3.7 31.6 - - - +
133L VAL* 4.5 9.4 - - + -
178L THR* 4.3 15.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
119H PRO* 3.6 29.6 - - + -
120H SER 3.4 4.7 - - - +
121H VAL* 4.5 2.7 - - + -
140H CYS* 4.9 1.1 - - - -
141H LEU* 1.3 79.2 - - - +
143H LYS* 1.3 59.6 + - - +
145H TYR* 3.9 16.3 - - + -
150H VAL* 4.4 5.6 - - + -
152H LEU* 3.7 30.3 - - + -
184H THR* 3.4 1.6 - - - -
185H LEU* 2.8 46.1 + - + +
208H VAL* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 3.6 1.7 - - - +
120H SER* 2.9 41.0 + - - -
122H TYR* 4.1 18.2 - - + -
141H LEU* 3.9 14.8 - - + -
142H VAL* 1.3 77.6 - - - +
144H GLY* 1.3 67.5 + - - +
145H TYR* 3.7 1.1 - - - -
183H TYR 3.6 2.5 - - - -
184H THR* 3.5 27.6 - - + +
124L GLN* 4.2 9.8 - - - +
131L SER* 4.1 13.9 - - - +
180L THR* 3.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H THR* 3.4 12.8 - - - +
118H ALA 3.1 18.1 - - - +
143H LYS* 1.3 82.2 - - - +
145H TYR* 1.3 57.2 + - - -
182H LEU* 3.8 27.7 - - - +
183H TYR 2.8 13.3 + - - -
184H THR* 4.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H THR 3.3 12.6 - - - +
119H PRO* 3.4 33.4 - - + -
142H VAL* 3.9 24.2 - - + -
144H GLY* 1.3 78.2 - - - +
146H PHE* 1.3 67.0 + - - +
147H PRO 3.6 18.8 - - - -
148H GLU* 2.8 28.0 + - - -
150H VAL* 3.7 17.8 - - + +
174H ALA* 3.2 17.2 - - - +
182H LEU* 3.6 3.8 - - - -
183H TYR* 2.8 63.9 + + + +
184H THR 4.3 0.7 - - - -
185H LEU* 3.8 13.2 - - + +
210H HIS* 3.7 7.0 - - - +
----------------------------------------------------------
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