Contacts of the strand formed by residues 251 - 259 (chain A) in PDB entry 5HMG
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 LEU 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A TRP* 4.0 14.8 - - + -
153A TRP* 4.3 0.7 - - - -
154A LEU* 3.6 31.9 + - + +
161A TYR* 3.7 10.8 + - - +
164A LEU* 4.3 7.2 - - + -
180A TRP* 4.9 6.5 - - + -
181A GLY 3.7 7.2 - - - +
202A VAL* 3.8 22.9 - - + -
245A ILE* 3.9 24.7 - - + -
247A SER* 3.7 24.2 - - - +
249A GLY 3.2 3.8 + - - -
250A ASN* 1.3 78.8 - - - +
252A ILE* 1.3 82.8 + - - +
253A ALA* 3.7 24.9 + - + +
254A PRO* 5.0 0.4 - - + -
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PHE* 4.0 16.4 - - + -
151A LEU* 3.8 41.1 - - + -
152A ASN 3.7 4.5 - - - +
153A TRP* 3.5 41.3 - - + +
180A TRP* 3.8 3.3 - - - +
181A GLY* 3.0 45.5 + - - +
182A ILE 4.1 12.1 - - - -
183A HIS* 4.1 9.9 - - + +
230A ILE* 4.3 13.7 - - + -
232A ILE* 5.8 0.2 - - + -
251A LEU* 1.3 78.7 - - - +
253A ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TRP* 3.5 35.4 - - + -
151A LEU* 3.5 5.8 - - - +
152A ASN* 2.7 50.6 + - + +
154A LEU* 4.2 4.5 - - + -
251A LEU* 3.7 17.2 - - + -
252A ILE* 1.3 73.9 - - - +
254A PRO* 1.3 69.2 - - + +
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Residues in contact with PRO 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 3.6 18.2 - - + +
127A TRP* 4.6 2.2 + - + -
150A ARG 4.3 3.1 - - - +
152A ASN* 4.9 1.4 - - - +
178A TYR* 4.2 19.7 - - + -
179A ILE 3.4 24.2 - - - +
180A TRP* 3.9 16.8 - - + -
243A LEU* 4.9 0.2 - - + -
245A ILE* 3.5 32.1 - - + -
251A LEU* 5.0 1.8 - - + -
253A ALA* 1.3 93.2 - - + +
255A ARG* 1.3 60.5 + - - +
256A GLY 3.6 15.3 + - - +
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Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 3.6 14.3 - - + -
122A THR* 3.3 17.9 - - + +
123A GLU 2.9 20.4 + - - +
125A PHE* 4.3 5.4 - - - -
132A GLN* 4.4 3.0 - - - +
133A ASN* 2.7 42.9 + - - +
147A PHE* 6.0 1.8 - - - +
148A PHE 4.7 2.4 + - - -
149A SER* 3.3 24.7 + - - +
150A ARG 3.3 20.9 + - - +
151A LEU 2.6 34.2 + - - -
152A ASN* 3.4 26.9 + - + +
254A PRO* 1.3 72.5 - - - +
256A GLY* 1.3 56.1 + - - +
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Residues in contact with GLY 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 3.4 11.7 - - - -
121A ILE 3.2 11.0 - - - -
123A GLU* 3.6 19.3 - - - -
125A PHE* 4.0 3.8 - - - -
178A TYR* 3.2 22.4 - - - -
179A ILE 5.1 1.2 + - - -
254A PRO* 3.3 10.1 + - - +
255A ARG* 1.3 77.9 + - - +
257A TYR* 1.3 59.0 + - - -
258A PHE* 5.5 0.2 - - - -
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Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A GLU 3.9 0.2 - - - +
120A PHE* 3.2 9.0 - - - -
121A ILE* 2.9 73.0 + - + +
123A GLU* 3.5 25.6 - - + -
172A ASP* 3.8 7.8 + - - -
174A PHE* 3.3 40.3 - + - -
176A LYS* 3.5 37.9 - - + -
177A LEU 3.6 11.4 - - - +
178A TYR* 4.0 9.2 - - + -
256A GLY* 1.3 73.5 - - - -
258A PHE* 1.3 73.1 + - - +
259A LYS* 4.1 4.7 - - + -
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Residues in contact with PHE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA 5.7 0.2 - - - -
70A LEU* 3.4 49.6 - - + -
71A LEU* 6.2 0.2 - - - -
117A THR 5.4 2.5 - - - +
118A LEU* 3.7 38.4 - - + -
119A GLU 3.5 2.7 - - - +
120A PHE* 3.9 22.2 - + + -
150A ARG* 3.8 22.0 - - + -
176A LYS* 3.8 0.3 - - - -
177A LEU* 2.9 62.2 + - + +
179A ILE* 3.8 19.7 - - + -
256A GLY 5.5 0.2 - - - -
257A TYR* 1.3 81.6 - - - +
259A LYS* 1.3 65.2 + - - +
260A MET* 5.8 0.2 - - + -
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Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A SER* 3.5 1.7 + - - -
117A THR* 3.1 21.5 - - - +
119A GLU* 3.2 37.9 + - + +
121A ILE* 4.5 11.4 - - + -
174A PHE* 3.2 50.5 - - - +
175A ASP 4.5 1.8 - - - -
257A TYR* 4.0 18.1 + - + -
258A PHE* 1.3 76.4 - - - +
260A MET* 1.3 68.4 + - - +
261A ARG* 3.8 22.2 - - - +
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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