Contacts of the strand formed by residues 140 - 150 (chain J) in PDB entry 5HHM
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 LYS 140 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163I MET* 3.9 20.0 - - + -
166I MET* 3.8 28.5 - - - +
168I PHE* 4.4 39.3 - - + +
134J GLU* 2.9 35.2 - - - +
135J ILE* 4.0 2.5 + - - +
138J THR* 3.4 35.4 + - - +
139J GLN* 1.3 79.7 - - - +
141J ALA* 1.3 56.4 + - - +
195J ARG* 3.8 18.2 - - + +
196J VAL 3.5 5.4 - - - +
197J SER* 4.9 2.2 - - - -
198J ALA* 4.0 3.1 - - - +
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Residues in contact with ALA 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J PRO* 3.7 20.6 - - + -
134J GLU* 3.5 1.6 - - - -
135J ILE* 4.8 4.0 - - + -
140J LYS* 1.3 71.8 - - - +
142J THR* 1.4 60.2 + - - +
143J LEU* 3.7 2.0 + - + +
194J LEU 3.5 2.4 - - - +
195J ARG* 3.2 3.1 - - - -
196J VAL* 2.6 45.3 + - + +
198J ALA* 4.2 5.8 - - - +
201J TRP* 3.6 34.1 - - + -
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Residues in contact with THR 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I LEU* 3.4 24.1 - - - +
135I LEU* 3.7 31.7 - - + +
137I THR* 5.8 1.1 - - - +
161I LEU* 5.1 1.6 - - + -
172I SER* 5.7 1.8 - - - +
130J PRO* 3.5 9.6 - - - +
134J GLU* 2.6 34.9 + - - +
141J ALA* 1.4 68.2 - - - +
143J LEU* 1.4 61.0 + - - +
144J VAL* 4.3 0.9 - - + -
193J ARG* 4.1 21.3 - - + -
194J LEU 3.3 10.3 - - - +
195J ARG* 2.8 27.0 + - + +
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Residues in contact with LEU 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J VAL* 4.3 16.4 - - + -
128J PHE 3.6 7.2 - - - +
129J GLU* 5.3 0.2 - - - -
130J PRO* 3.7 17.5 - - + -
141J ALA 4.0 9.4 - - - +
142J THR* 1.4 70.0 - - - +
144J VAL* 1.3 60.8 + - - +
159J TRP* 3.5 20.7 - - + -
193J ARG* 3.6 2.1 - - - -
194J LEU* 2.7 45.7 + - + +
196J VAL* 4.2 17.7 - - + -
201J TRP* 4.0 15.9 - - + -
208J PHE* 3.5 45.5 - - + -
239J ALA* 4.8 1.3 - - + -
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Residues in contact with VAL 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I LEU* 3.7 24.7 - - + -
133I VAL* 4.4 8.3 - - + -
135I LEU* 3.8 28.9 - - + -
174I VAL* 3.8 35.2 - - + -
127J VAL* 3.7 1.4 - - - -
128J PHE* 2.8 45.6 + - + -
142J THR* 4.0 7.0 - - + +
143J LEU* 1.3 77.8 - - - +
145J CYS* 1.3 69.7 + - - +
146J LEU* 5.6 0.9 - - + -
159J TRP* 4.2 1.8 - - - -
192J SER 3.6 7.9 - - - +
193J ARG* 4.5 1.6 - - + -
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Residues in contact with CYS 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J VAL* 3.9 11.0 - - - -
126J ALA 3.5 10.1 - - - +
127J VAL* 4.7 0.4 - - + -
144J VAL* 1.3 77.2 - - - +
146J LEU* 1.3 77.0 + - - +
147J ALA 4.6 0.2 - - - -
157J LEU* 4.2 10.8 - - - -
159J TRP* 3.5 21.2 - - + -
191J SER* 3.2 11.2 - - - -
192J SER* 2.8 34.5 + - - +
210J CYS* 2.4 42.8 - - + -
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Residues in contact with LEU 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I VAL* 3.8 22.0 - - + -
174I VAL* 5.5 1.8 - - + -
176I TRP* 3.5 61.7 - - + +
124J GLU 3.3 5.2 - - - +
125J VAL* 3.4 1.4 - - - -
126J ALA* 3.0 31.1 + - + +
128J PHE* 3.7 20.6 - - + -
144J VAL* 5.6 0.9 - - + -
145J CYS* 1.3 82.5 - - - +
147J ALA* 1.3 59.8 + - - +
148J THR* 3.9 16.8 - - + -
190J LEU 3.5 13.7 - - - +
191J SER* 4.1 7.0 - - - -
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Residues in contact with ALA 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J PRO* 4.2 11.9 - - + -
124J GLU 3.4 7.0 - - - -
125J VAL* 4.6 1.1 - - + +
145J CYS* 4.6 0.6 - - - -
146J LEU* 1.3 71.4 - - - +
148J THR* 1.3 61.2 + - - +
150J PHE* 3.4 18.2 - - + -
157J LEU* 4.5 4.7 - - + -
189J SER* 3.1 3.1 - - - -
190J LEU* 2.6 47.7 + - + +
212J VAL* 4.3 25.1 - - + -
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Residues in contact with THR 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176I TRP* 4.3 9.2 - - - +
123J PRO* 3.4 2.1 - - - +
124J GLU* 3.0 48.7 + - - +
146J LEU* 3.9 29.2 - - + -
147J ALA* 1.3 78.1 - - - +
149J GLY* 1.3 64.1 - - - +
150J PHE 3.3 4.7 + - - -
179J GLU* 3.2 9.2 - - - +
188J TYR 3.4 2.2 - - - -
189J SER* 3.2 16.6 - - - +
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Residues in contact with GLY 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J PHE* 3.4 10.0 - - - +
122J PRO 3.7 4.9 - - - +
124J GLU* 5.9 1.8 - - - -
148J THR* 1.3 71.5 - - - +
150J PHE* 1.4 57.4 + - - -
179J GLU* 2.7 30.7 + - - -
187J ARG* 2.8 41.4 + - - -
188J TYR 2.9 5.1 + - - -
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Residues in contact with PHE 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J PHE 3.4 7.2 - - - +
122J PRO 4.1 0.2 - - - -
123J PRO* 3.7 39.3 - - + -
147J ALA* 3.4 31.6 - - + -
148J THR 3.3 0.2 - - - -
149J GLY* 1.4 77.4 - - - +
151J TYR* 1.3 59.7 + - - +
152J PRO 3.5 14.6 - - - -
153J ASP* 3.7 15.0 - - + -
155J VAL* 3.6 36.1 - - + -
176J PRO* 4.4 4.9 - - + -
187J ARG* 3.4 0.6 - - - -
188J TYR* 2.6 68.6 + - + -
189J SER 4.2 0.9 - - - -
190J LEU* 3.9 15.0 - - + -
214J PHE* 4.3 3.4 - - + -
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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