Contacts of the strand formed by residues 199 - 207 (chain B) in PDB entry 1HXD
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 ALA 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B TRP 3.7 0.5 - - - +
138B ARG* 3.2 4.0 - - - +
139B LEU* 2.3 54.7 + - + +
142B GLY* 3.7 5.6 - - - +
143B PRO* 3.6 30.3 - - + -
144B ALA 5.1 0.2 - - - +
191B LEU* 5.8 3.8 - - + -
192B THR 3.5 9.6 - - - +
193B GLY* 4.6 1.1 - - - -
197B ASP 3.9 0.2 + - - -
198B ALA* 1.3 74.9 - - - +
200B GLN* 1.3 61.4 + - - +
201B ILE* 3.9 8.2 + - + -
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Residues in contact with GLN 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 5.5 2.1 - - + +
98B ILE* 4.6 26.7 + - + +
99B GLY* 6.1 0.4 - - - -
136B PHE* 3.4 31.5 - - + -
137B TRP 3.5 4.0 - - - -
138B ARG* 3.0 40.5 + - - +
190B GLU 3.5 1.7 - - - +
191B LEU* 3.4 3.8 - - - -
192B THR* 3.1 50.6 + - + +
198B ALA 4.4 5.3 + - - +
199B ALA* 1.3 73.5 - - - +
201B ILE* 1.3 63.4 + - - +
202B VAL* 5.2 1.9 - - - +
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B MET 3.5 0.5 - - - +
136B PHE* 3.2 7.0 - - - -
137B TRP* 2.5 59.4 + - + +
139B LEU* 3.1 46.0 - - + +
145B ALA* 5.8 0.4 - - + -
146B ALA* 6.3 3.1 - - - +
149B LEU* 5.0 14.1 - - + -
189B VAL* 3.4 31.6 - - + -
190B GLU 3.3 5.2 - - - +
191B LEU* 4.8 9.2 - - + -
199B ALA* 4.2 4.9 - - + +
200B GLN* 1.3 77.8 - - - +
202B VAL* 1.3 65.4 - - - +
203B ILE* 3.7 18.6 - - + -
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASN* 3.5 45.3 - - + +
94B LEU* 4.3 11.9 - - + -
95B LEU* 3.5 35.7 - - + +
98B ILE* 4.2 6.7 - - + -
135B MET 3.4 5.6 - - - +
136B PHE* 4.1 16.4 - - + -
188B LEU 4.0 0.5 - - - +
189B VAL* 3.6 1.9 - - - -
190B GLU* 2.7 43.0 + - - +
200B GLN 5.2 0.7 - - - +
201B ILE* 1.3 76.3 - - - +
203B ILE* 1.3 65.4 + - - +
204B GLY 4.0 0.5 + - - -
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASN* 3.8 2.9 - - - -
133B LEU* 5.0 2.3 - - + +
134B SER* 3.0 2.1 - - - -
135B MET* 2.6 58.4 + - + +
137B TRP* 3.9 22.7 - - + +
149B LEU* 4.8 9.4 - - + -
153B ILE* 4.2 31.2 - - + -
187B ILE* 5.0 0.7 - - + -
188B LEU 4.2 2.2 - - - -
189B VAL* 4.1 18.4 - - + -
201B ILE* 3.7 24.9 - - + +
202B VAL* 1.3 78.9 - - - +
204B GLY* 1.3 62.6 + - - +
205B ALA* 4.4 2.6 + - + +
246B LEU* 5.6 5.8 - - + -
250B LEU* 4.6 10.5 - - + -
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Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASN* 2.9 25.7 + - - +
133B LEU 3.4 5.6 - - - -
134B SER* 3.7 0.7 - - - -
186B GLY 4.1 0.5 - - - +
187B ILE* 3.4 5.5 - - - +
188B LEU 2.8 41.6 + - - -
203B ILE* 1.3 72.4 - - - +
205B ALA* 1.3 60.1 + - - +
501B BTN 3.8 10.0 - - - +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 3.1 7.0 - - + +
133B LEU* 2.8 52.5 + - + +
153B ILE* 5.7 2.0 - - + -
157B MET* 4.1 32.3 - - + -
186B GLY 3.6 4.5 - - - +
187B ILE* 5.0 4.9 - - + -
203B ILE* 4.4 2.2 - - + +
204B GLY* 1.3 74.8 - - - +
206B GLY* 1.3 59.2 + - - +
207B ILE* 4.1 4.3 - - + -
501B BTN 3.5 6.7 - - - +
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TRP* 3.7 18.5 - - - -
131B LEU 3.1 6.5 - - - -
185B ALA* 3.1 7.5 - - - +
186B GLY 2.9 36.7 + - - -
205B ALA* 1.3 74.7 - - - +
207B ILE* 1.4 60.8 + - - -
501B BTN 3.3 18.1 - - - +
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASN* 3.1 5.1 - - - +
131B LEU* 2.8 61.0 + - + +
157B MET* 4.4 17.7 - - + -
161B LEU* 4.8 15.9 - - + -
184B LEU* 5.1 4.5 - - + +
185B ALA* 3.9 19.3 - - + -
205B ALA* 5.5 2.5 - - + -
206B GLY* 1.4 72.3 - - - -
208B ASN* 1.3 64.2 + - - +
209B MET* 3.1 27.6 - - + +
226B LEU* 4.6 9.6 - - + -
238B LEU* 4.3 12.1 - - + -
242B LEU* 4.2 15.5 - - + -
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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