Contacts of the strand formed by residues 135 - 140 (chain H) in PDB entry 2FD6
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 CYS 135 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H VAL* 3.6 20.9 - - - -
122H TYR 3.5 8.5 - - - -
123H PRO* 4.8 0.2 - - - -
124H LEU* 3.5 9.1 - - - +
134H GLY* 1.1 85.2 - - - +
136H LEU* 1.3 60.0 + - - +
137H VAL* 4.0 5.7 + - + +
147H VAL* 4.8 2.5 - - + -
149H TRP* 3.4 9.0 - - + -
173H SER* 3.2 6.1 - - - -
174H SER* 2.8 32.0 + - - +
190H CYS* 2.0 44.6 - - + -
192H VAL* 4.0 10.8 - - - -
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Residues in contact with LEU 136 (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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120H SER 3.2 5.7 - - - +
121H VAL* 3.6 0.9 - - - -
122H TYR* 2.7 64.9 + - + +
124H LEU* 3.9 16.6 - - + +
135H CYS* 1.3 72.5 - - - +
137H VAL* 1.3 59.4 + - - +
138H LYS* 4.3 10.1 - - + -
171H THR* 3.7 21.1 - - + -
172H LEU 3.6 14.1 - - - +
173H SER* 4.4 10.1 - - - -
123L GLN* 4.4 2.9 - - - +
130L SER* 3.9 29.6 - - - +
132L VAL* 4.4 16.2 - - + -
177L THR* 4.7 8.1 - - + +
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Residues in contact with VAL 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 3.4 32.3 - - + -
120H SER 3.6 3.8 - - - +
121H VAL* 4.9 2.0 - - + -
135H CYS* 4.6 8.1 - - - +
136H LEU* 1.3 73.0 - - - +
138H LYS* 1.3 58.4 + - - +
140H TYR* 3.5 16.8 - - + -
145H VAL* 4.4 5.4 - - + -
147H VAL* 4.1 6.7 - - + -
171H THR* 3.2 4.0 - - - -
172H LEU* 2.7 62.8 + - + +
174H SER* 6.3 0.2 - - - -
192H VAL* 3.9 32.8 - - + -
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Residues in contact with LYS 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 3.7 0.8 - - - +
120H SER* 2.9 40.8 + - - -
122H TYR* 4.2 19.7 - - + -
136H LEU* 4.3 9.0 - - + -
137H VAL* 1.3 74.6 - - - +
139H GLY* 1.3 67.7 + - - +
140H TYR 3.7 1.6 - - - -
166H GLN* 3.2 35.6 + - - +
167H SER* 5.5 2.6 + - - -
170H TYR 4.0 1.3 - - - -
171H THR* 3.8 15.9 + - + +
123L GLN* 3.8 27.8 - - - +
128L GLY* 6.4 0.9 - - - -
130L SER* 4.1 10.5 - - - +
179L THR* 4.7 6.2 - - - +
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Residues in contact with GLY 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H THR* 3.4 15.2 - - - +
118H PRO 3.3 14.3 - - - +
120H SER* 5.4 0.3 + - - -
138H LYS* 1.3 82.3 - - - +
140H TYR* 1.3 56.9 + - - -
166H GLN 5.6 0.9 - - - -
169H LEU* 3.6 26.7 - - - +
170H TYR 2.9 13.4 + - - -
171H THR* 3.9 1.2 + - - -
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Residues in contact with TYR 140 (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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117H THR 3.3 11.2 - - - +
119H PRO* 3.3 24.7 - - + -
137H VAL* 3.5 38.8 - - + -
139H GLY* 1.3 77.2 - - - +
141H PHE* 1.3 67.0 + - - +
142H PRO 3.7 16.8 - - - -
143H GLU* 3.2 19.7 + - - -
145H VAL* 3.8 21.0 - - + +
163H ALA* 3.0 27.2 - - - +
169H LEU* 3.8 2.4 - - - -
170H TYR* 2.9 64.6 + + + -
172H LEU* 3.6 16.7 - - + +
194H HIS* 4.0 2.2 - - - +
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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