Contacts of the strand formed by residues 148 - 155 (chain H) in PDB entry 4XX1
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 THR 148 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B ARG* 4.2 12.1 - - - +
147H GLY* 1.3 79.2 - - - +
149H ALA* 1.3 77.0 + - - +
196H THR* 4.8 8.3 - - - +
197H VAL 3.2 11.9 + - - -
198H PRO* 4.1 1.6 - - - -
199H SER* 2.6 25.6 + - - +
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Residues in contact with ALA 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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139H PRO* 5.6 4.7 - - + -
148H THR* 1.3 88.4 + - - +
150H ALA* 1.3 66.5 + - - +
196H THR* 3.7 3.1 - - - +
197H VAL* 2.7 35.5 + - + +
199H SER* 4.3 13.0 - - - -
202H LEU* 4.3 18.8 - - + -
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Residues in contact with ALA 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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139H PRO* 4.7 10.2 - - - +
149H ALA* 1.3 80.5 - - - +
151H LEU* 1.3 62.8 + - - +
194H VAL* 5.5 4.7 - - + -
195H VAL 3.7 18.2 - - - +
196H THR* 4.7 5.6 - - + -
197H VAL* 4.7 1.1 - - - +
117L THR* 5.3 12.5 - - + +
119L PHE* 3.7 18.3 - - + -
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Residues in contact with LEU 151 (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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137H LEU 3.7 15.9 - - - +
139H PRO* 4.2 16.6 - - + -
150H ALA* 1.3 73.4 - - - +
152H GLY* 1.3 68.7 + - - +
167H TRP* 3.6 28.9 - - + -
194H VAL* 3.2 28.3 - - - +
195H VAL* 3.5 16.9 + - + +
197H VAL* 4.5 8.9 - - + +
202H LEU* 4.1 20.0 - - + -
207H TYR* 4.0 31.4 - - + -
224H VAL* 3.6 26.2 - - + +
119L PHE* 4.4 2.9 - - - -
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Residues in contact with GLY 152 (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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137H LEU* 2.7 34.5 + - - -
151H LEU* 1.3 81.0 - - - +
153H CYS* 1.3 56.1 + - - -
167H TRP* 3.4 16.2 - - - -
193H SER 3.2 13.7 - - - -
194H VAL* 4.1 4.7 - - - -
224H VAL* 3.3 14.0 - - - +
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Residues in contact with CYS 153 (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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134H VAL* 4.4 6.7 - - + -
135H PHE 3.1 16.6 - - - +
136H PRO* 4.1 2.2 - - + -
137H LEU* 3.6 9.0 - - - +
152H GLY* 1.3 73.7 - - - +
154H LEU* 1.3 58.5 + - - +
155H VAL* 4.4 3.3 + - - +
165H VAL* 4.7 9.2 - - - -
167H TRP* 3.7 7.0 - - - -
192H SER* 3.9 0.9 - - - -
193H SER* 3.1 30.8 + - - +
209H CYS* 2.0 53.6 - - - -
211H VAL* 4.8 1.8 - - - -
222H LYS* 3.7 9.2 - - - +
224H VAL* 4.3 1.1 - - + -
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Residues in contact with LEU 154 (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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133H SER 4.3 0.2 - - - +
134H VAL* 3.2 5.4 - - - +
135H PHE* 2.7 55.0 + - + +
137H LEU* 3.8 21.5 - - + +
153H CYS* 1.3 75.6 - - - +
155H VAL* 1.3 78.4 + - - +
156H LYS 3.9 0.3 + - - -
190H SER* 5.3 2.5 - - - -
191H HIS 3.5 15.0 - - - +
192H SER* 3.6 13.2 - - - +
132L THR* 3.6 28.5 - - + +
134L VAL* 3.7 21.3 - - + -
178L TYR* 4.7 11.4 - - + -
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Residues in contact with VAL 155 (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* 3.5 28.5 - - + -
134H VAL* 4.2 15.9 - - + -
153H CYS* 5.1 3.8 - - - +
154H LEU* 1.3 85.4 - - - +
156H LYS* 1.3 67.4 + - - +
158H TYR* 3.5 20.0 - - + -
163H VAL* 4.5 12.6 - - + -
165H VAL* 4.8 6.3 - - + -
190H SER* 3.3 18.0 + - - -
191H HIS* 3.2 43.0 + - + +
192H SER* 5.5 0.4 - - - -
211H VAL* 5.1 4.0 - - + -
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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