Contacts of the strand formed by residues 179 - 188 (chain A) in PDB entry 4HC1
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A VAL* 4.3 7.3 - - - +
132A GLY 4.7 2.4 + - - -
177A PRO* 3.2 6.4 - - - +
178A PRO* 1.3 85.7 - - + +
180A LEU* 1.3 72.1 + - - +
181A TYR* 4.0 31.9 - - + +
198A ALA* 5.1 1.8 - - + -
199A ILE 3.5 17.0 - - - +
200A PRO* 3.6 11.4 - - + -
201A VAL* 3.8 5.8 - - - +
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Residues in contact with LEU 180 (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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103A LEU* 3.7 22.9 - - + -
129A LEU* 4.3 14.1 - - + -
130A LEU 3.6 5.2 - - - +
131A VAL* 3.7 32.3 - - + -
136A LEU* 3.8 28.0 - - + -
169A LEU* 4.1 9.2 - - + -
172A LEU* 4.1 14.4 - - + -
177A PRO* 4.5 10.3 - - + -
179A ALA* 1.3 78.5 - - - +
181A TYR* 1.3 61.6 + - - +
198A ALA 3.6 0.2 - - - -
199A ILE* 2.6 52.0 + - + +
201A VAL* 4.0 9.6 - - + +
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Residues in contact with TYR 181 (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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129A LEU* 3.5 5.3 - - - -
130A LEU* 2.7 54.4 + - + +
132A GLY* 5.1 10.1 - - - -
133A GLY 5.9 1.6 - - - -
179A ALA* 4.0 25.4 - - + +
180A LEU* 1.3 75.8 - - - +
182A CYS* 1.3 62.0 + - - +
196A ARG* 4.2 26.7 - - + -
197A GLN 3.5 5.4 - - - -
198A ALA* 3.3 38.0 - - + +
42B ASP* 5.7 4.7 - - - -
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Residues in contact with CYS 182 (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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96A LEU* 3.9 2.4 - - - +
98A VAL* 4.3 3.8 - - + -
112A CYS* 2.0 57.7 - - + -
127A PHE* 4.2 7.9 - - - -
128A SER 3.8 3.1 - - - -
129A LEU* 4.3 6.3 - - + -
167A TRP* 3.9 12.3 - - + -
181A TYR* 1.3 71.4 - - - +
183A GLN* 1.3 63.3 + - - +
195A HIS 3.7 0.5 - - - +
196A ARG* 3.2 4.6 - - - +
197A GLN 2.9 34.8 + - - +
199A ILE* 3.9 18.4 - - + +
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Residues in contact with GLN 183 (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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126A SER 4.0 0.2 - - - +
127A PHE* 3.5 5.9 - - - -
128A SER* 2.8 55.3 + - - +
130A LEU* 3.6 22.3 - - + +
181A TYR 3.7 0.2 + - - -
182A CYS* 1.3 76.3 - - - +
184A ALA* 1.3 61.4 + - - +
185A THR* 3.9 19.1 + - - +
194A SER* 3.8 16.3 + - - -
195A HIS 3.2 11.2 - - - +
196A ARG* 3.3 40.1 - - + +
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Residues in contact with ALA 184 (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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92A PHE* 3.2 25.2 - - + -
96A LEU* 4.0 22.1 - - + +
114A ALA* 4.8 2.2 - - + -
125A LEU* 4.8 1.6 - - + -
126A SER 3.7 4.3 - - - +
127A PHE* 3.8 25.8 - - + -
182A CYS 4.2 0.4 - - - -
183A GLN* 1.3 72.7 - - - +
185A THR* 1.3 62.0 + - - +
194A SER* 3.2 1.4 - - - -
195A HIS 2.8 32.6 + - - +
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Residues in contact with THR 185 (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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92A PHE* 4.4 0.2 - - - -
124A ALA 3.3 1.8 - - - +
125A LEU* 3.4 5.6 - - - +
126A SER* 2.8 52.4 + - - +
128A SER* 4.9 2.9 + - - -
183A GLN* 3.9 22.4 + - - +
184A ALA* 1.3 75.3 + - - +
186A MET* 1.3 64.5 + - - +
187A ARG* 4.5 5.4 - - + +
192A GLU* 3.3 36.6 - - + +
193A LEU 3.4 10.3 - - - +
194A SER* 4.0 5.0 - - - -
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Residues in contact with MET 186 (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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90A TYR* 4.3 12.3 - - - -
92A PHE* 3.9 35.1 - - + -
117A VAL* 3.6 22.2 - - + -
118A THR 4.0 4.5 - - - +
119A PRO* 3.3 48.5 - - + +
124A ALA* 3.2 7.2 - - + +
125A LEU* 4.0 11.9 - - + +
185A THR* 1.3 72.6 - - - +
187A ARG* 1.3 64.6 + - - +
188A LEU* 3.8 20.6 + - + +
191A LEU 3.9 0.3 - - - +
192A GLU* 3.6 1.6 - - - -
193A LEU* 2.8 36.9 + - + +
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Residues in contact with ARG 187 (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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122A PRO 4.8 4.4 + - - -
123A ASN* 4.1 21.9 + - - +
124A ALA* 2.7 30.9 + - - +
126A SER* 3.8 28.5 + - - -
185A THR* 4.5 3.5 - - + +
186A MET* 1.3 71.5 - - - +
188A LEU* 1.3 69.3 + - - +
191A LEU 3.9 4.0 - - - +
192A GLU* 3.7 32.6 + - + +
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Residues in contact with LEU 188 (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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14A ALA* 4.5 5.4 - - + -
88A LEU* 3.9 27.4 - - + -
90A TYR* 3.4 53.6 - - + +
119A PRO* 4.8 4.9 - - + -
186A MET* 4.1 19.1 - - + +
187A ARG* 1.3 82.2 - - - +
189A PRO* 1.3 78.1 - - + +
190A GLY 2.9 5.4 + - - -
191A LEU* 2.8 33.8 + - + +
193A LEU* 4.4 12.3 - - + -
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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