Contacts of the strand formed by residues 140 - 150 (chain H) in PDB entry 4YXH
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 MET 140 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138H ASN* 2.6 72.6 + - + +
139H SER* 1.3 69.4 + - - +
141H VAL* 1.3 61.0 + - - +
142H THR* 5.5 0.3 - - - +
187H THR* 4.4 14.3 - - + +
188H VAL 4.0 5.2 - - - -
189H PRO* 5.6 0.4 - - - -
114L THR* 6.2 4.7 - - - -
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Residues in contact with VAL 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H PRO* 6.3 2.5 - - + -
135H GLY 5.1 9.9 - - - +
138H ASN* 4.0 11.7 - - - +
139H SER* 3.2 9.2 + - - +
140H MET* 1.3 75.9 - - - +
142H THR* 1.3 62.6 + - - +
143H LEU* 4.7 14.8 - - + -
187H THR* 3.1 7.8 - - - +
188H VAL* 3.0 43.7 + - + +
189H PRO 4.4 1.3 - - - +
190H SER* 4.2 23.1 - - - +
193H TRP* 5.0 11.0 - - + +
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Residues in contact with THR 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H PRO* 5.1 5.6 - - - +
140H MET 5.5 0.7 - - - +
141H VAL* 1.3 76.7 - - - +
143H LEU* 1.3 64.1 + - - +
185H SER* 5.5 5.2 - - - -
186H VAL 3.0 10.3 - - - +
187H THR* 2.9 31.2 - - + +
114L THR* 5.1 10.3 - - - +
116L SER* 3.1 28.2 + - - -
118L PHE* 3.1 21.1 - - - -
135L PHE* 5.8 1.6 - - - -
137L ASN* 5.3 7.2 - - - +
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Residues in contact with LEU 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H LEU 5.1 0.7 - - - -
131H ALA* 5.9 1.3 - - + +
132H PRO* 5.5 4.5 - - + -
141H VAL* 4.7 12.3 - - + -
142H THR* 1.3 83.6 - - - +
144H GLY* 1.3 59.7 + - - +
159H TRP* 4.1 1.6 - - - -
185H SER* 3.8 1.9 - - - -
186H VAL* 2.9 41.8 + - + +
188H VAL* 4.9 8.1 - - + -
193H TRP* 3.8 40.6 - - + -
198H VAL* 2.9 47.1 - - + -
215H ILE* 3.2 23.3 - - + -
118L PHE* 4.3 4.3 - - - -
135L PHE* 5.4 0.2 - - - -
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Residues in contact with GLY 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H LEU* 3.2 38.2 + - - +
143H LEU* 1.3 78.5 - - - +
145H CYS* 1.3 71.8 + - - -
159H TRP* 4.1 1.3 - - - -
184H SER 3.5 8.7 - - - -
185H SER* 4.7 1.1 - - - -
215H ILE* 4.0 5.9 - - - +
118L PHE* 4.1 13.3 - - - -
135L PHE* 4.9 3.8 - - - -
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Residues in contact with CYS 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H TYR 4.1 4.3 - - - +
129H PRO* 4.9 5.2 - - - -
130H LEU* 5.5 1.1 - - - -
144H GLY* 1.3 80.1 - - - -
146H LEU* 1.3 61.9 + - - +
147H VAL* 4.0 7.4 + - + +
157H VAL* 5.8 0.4 - - + -
159H TRP* 3.5 7.4 - - + -
183H SER* 3.5 5.7 - - - -
184H SER* 2.9 40.6 + - - +
200H CYS* 2.6 48.9 - - + -
202H VAL* 5.7 4.3 - - + -
213H LYS* 5.3 4.5 - - - -
215H ILE* 4.4 11.4 - - - -
135L PHE* 5.5 1.3 - - - -
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Residues in contact with LEU 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H SER 3.9 0.3 - - - +
127H VAL* 3.6 2.3 - - - -
128H TYR* 3.0 47.5 + - + +
130H LEU* 3.8 28.1 - - + +
145H CYS* 1.3 73.6 - - - +
147H VAL* 1.3 62.6 + - - +
148H LYS* 3.8 12.9 + - + -
181H THR* 4.2 16.4 - - + -
182H LEU 3.2 21.5 - - - +
183H SER* 4.7 7.2 - - - +
124L GLN* 4.5 14.1 - - - +
131L SER* 3.9 28.7 - - - +
133L VAL* 4.3 12.6 - - + -
178L THR* 5.3 6.7 - - + +
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Residues in contact with VAL 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H PRO* 3.5 31.6 - - + -
126H SER 4.0 1.6 - - - +
127H VAL* 4.7 7.9 - - + +
145H CYS* 4.8 9.0 - - + +
146H LEU* 1.3 76.8 - - - +
148H LYS* 1.3 57.8 + - - +
150H TYR* 3.8 15.1 - - + -
155H VAL* 4.2 12.8 - - + -
157H VAL* 4.9 11.0 - - + -
181H THR* 3.4 3.3 - - - +
182H LEU* 3.0 48.5 + - + +
183H SER* 5.7 1.8 - - - -
184H SER* 6.0 1.1 - - - -
202H VAL* 4.3 25.4 - - + -
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Residues in contact with LYS 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H PRO* 3.7 0.9 - - - +
126H SER* 3.0 40.3 + - - +
128H TYR* 5.3 2.9 - - + -
146H LEU* 3.8 15.0 + - + +
147H VAL* 1.3 75.6 - - - +
149H GLY* 1.3 65.6 + - - +
150H TYR* 3.6 2.2 - - - -
176H GLN* 3.2 27.1 - - - +
177H SER* 6.0 0.7 - - - -
181H THR* 3.6 17.5 - - + +
124L GLN* 3.8 22.9 - - - +
129L GLY* 5.8 2.6 - - - -
130L ALA 5.7 2.0 - - - +
131L SER* 3.2 21.9 + - - +
180L THR* 3.8 13.9 - - + +
181L LEU 5.8 1.6 + - - -
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Residues in contact with GLY 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H THR* 3.3 22.7 - - - +
124H PRO 3.5 5.4 - - - +
125H PRO* 4.3 0.2 - - - -
126H SER 4.7 0.7 + - - -
148H LYS* 1.3 81.1 - - - +
150H TYR* 1.3 56.1 + - - -
176H GLN 5.8 0.4 - - - -
179H LEU* 3.5 26.3 - - - +
180H TYR 2.9 15.9 + - - -
181H THR* 3.7 2.1 + - - -
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Residues in contact with TYR 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H THR 3.2 11.7 - - - +
125H PRO* 3.4 25.1 - - + -
147H VAL* 3.8 31.2 - - + -
149H GLY* 1.3 77.8 - - - +
151H PHE* 1.3 62.8 + - - +
152H PRO 3.5 11.9 - - - -
153H GLU* 3.9 21.1 - - - +
155H VAL* 3.7 19.5 - - + +
179H LEU* 3.9 2.3 - - - +
180H TYR* 2.8 71.8 + - + +
181H THR 4.0 0.7 - - - -
182H LEU* 2.7 34.6 - - + +
204H HIS* 3.2 21.5 - + + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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