Contacts of the strand formed by residues 115 - 124 (chain A) in PDB entry 2HU4
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 PHE 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A SER* 5.5 0.3 + - - -
113A ASP 4.1 0.4 + - - -
114A VAL* 1.3 89.3 - - - +
116A VAL* 1.3 61.4 + - - +
117A ILE* 3.8 20.9 + - + +
133A PHE* 4.3 2.9 - + - -
135A THR* 3.9 21.3 - - + -
137A GLY* 5.3 1.3 - - - -
138A ALA 3.5 17.5 - - - -
139A LEU* 3.8 10.2 - - + +
140A LEU* 4.1 5.4 - - - +
159A MET* 3.7 32.1 - - + -
167A PRO* 2.8 15.6 + - + +
168A SER* 3.4 39.3 - - - -
169A PRO* 3.7 17.3 - - + -
171A SER* 4.1 7.0 - - - -
440A SER* 4.3 1.7 + - - -
108D ILE* 3.7 29.2 - - + -
166D ALA 6.4 0.2 - - - -
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Residues in contact with VAL 116 (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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114A VAL 3.7 0.2 + - - -
115A PHE* 1.3 72.4 - - - +
117A ILE* 1.3 70.8 + - - +
135A THR* 3.4 1.7 - - - -
136A GLN* 3.1 38.3 + - + -
138A ALA* 3.0 30.8 + - + +
139A LEU 4.4 2.7 - - - +
140A LEU* 4.3 15.3 - - + -
145A SER* 4.6 6.7 - - - +
148A THR* 4.1 18.4 - - + +
439A THR 3.2 27.6 - - - +
440A SER* 3.4 12.8 - - - -
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Residues in contact with ILE 117 (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 ASP* 6.0 1.3 - - - +
105A SER* 5.5 0.4 - - - +
115A PHE* 3.8 15.9 - - + +
116A VAL* 1.3 85.6 - - - +
118A ARG* 1.3 65.6 + - - +
120A PRO* 4.3 16.4 - - + -
131A THR* 6.4 0.2 - - + -
133A PHE* 3.7 44.0 - - + -
134A LEU 3.4 11.4 - - - +
135A THR* 3.8 7.9 - - - +
136A GLN* 5.0 2.2 - - - -
156A ARG* 4.7 0.9 - - - -
167A PRO* 4.1 17.7 - - + -
439A THR 4.9 0.4 - - - -
440A SER* 2.8 17.8 + - - +
441A GLY 3.0 44.1 + - - +
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Residues in contact with ARG 118 (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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117A ILE* 1.3 83.0 - - - +
119A GLU* 1.3 109.1 + - - +
120A PRO* 3.4 5.4 - - - +
134A LEU 3.3 19.3 + - - +
136A GLN* 5.5 0.7 - - - +
148A THR 5.3 4.5 - - - +
151A ASP* 5.2 2.2 + - - -
156A ARG* 3.4 9.8 - - - +
371A ARG* 5.0 0.4 - - - +
406A TYR* 3.7 17.0 - - - -
425A GLU* 2.6 43.7 + - - -
427A ILE* 3.4 23.8 - - - +
439A THR* 4.0 31.9 - - + +
440A SER 4.5 3.8 - - - -
441A GLY 5.1 0.2 - - - +
800A G39 3.6 26.9 + - - +
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Residues in contact with GLU 119 (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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118A ARG* 1.3 100.0 + - - +
120A PRO* 1.3 64.8 - - - +
121A PHE* 4.0 11.4 - - - -
133A PHE* 3.9 9.7 - - - -
134A LEU* 3.8 18.4 + - + +
151A ASP* 4.7 0.3 - - - +
156A ARG* 2.9 32.2 + - - -
227A GLU* 3.8 31.6 - - + +
406A TYR* 4.0 26.2 - - + -
423A TRP* 5.8 0.2 - - - -
425A GLU* 3.0 13.5 + - - -
800A G39 2.9 26.6 + - - +
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Residues in contact with PRO 120 (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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117A ILE* 4.3 19.7 - - + -
118A ARG* 3.5 3.1 - - - -
119A GLU* 1.3 90.9 - - - +
121A PHE* 1.3 66.0 + - - +
131A THR* 4.8 8.5 - - + -
132A PHE 3.3 11.4 - - - +
133A PHE* 4.2 2.5 - - + -
423A TRP* 3.1 24.3 - - + -
425A GLU* 3.3 39.3 - - + +
441A GLY* 5.9 2.0 - - - +
442A SER 4.8 2.7 - - - +
443A SER* 4.6 17.3 - - - -
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Residues in contact with PHE 121 (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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119A GLU 4.0 9.0 - - - -
120A PRO* 1.3 79.5 - - - +
122A ILE* 1.3 70.7 + - - +
123A SER* 4.6 1.8 - - - -
131A THR* 3.4 3.6 - - - +
132A PHE* 2.8 71.5 + + + +
134A LEU* 6.4 0.9 - - + -
158A LEU* 4.7 7.9 - - + -
180A ALA* 4.5 5.4 - - + -
181A SER* 3.9 10.3 - - - -
182A ALA* 3.8 25.1 - - + -
227A GLU* 3.6 17.0 - - - +
228A SER* 3.4 37.0 - - - -
229A GLU* 3.7 4.3 - - - -
423A TRP* 3.5 28.0 - - + +
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Residues in contact with ILE 122 (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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100A TYR* 5.3 0.2 - - + -
101A SER* 4.3 4.5 - - - +
121A PHE* 1.3 83.8 - - - +
123A SER* 1.3 72.1 + - - +
129A CYS* 4.4 4.3 - - + -
130A ARG 3.2 10.8 - - - +
131A THR* 3.8 11.7 - - + +
163A VAL* 3.6 29.2 - - + -
229A GLU* 3.9 3.8 + - - +
410A PHE* 3.2 54.4 - - + +
423A TRP* 3.6 18.0 + - + -
443A SER* 5.6 7.2 - - - +
444A ILE 5.4 0.7 - - - +
445A SER* 3.5 34.8 - - - +
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Residues in contact with SER 123 (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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121A PHE* 4.6 1.8 - - - -
122A ILE* 1.3 78.7 - - - +
124A CYS* 1.3 66.8 + - - +
129A CYS* 3.5 0.2 - - - -
130A ARG 2.8 29.4 + - - +
132A PHE* 4.0 11.4 - - - -
182A ALA 3.7 11.2 + - - -
183A CYS* 3.8 5.5 - - - +
184A HIS 4.5 0.3 + - - -
189A TRP* 3.4 29.9 - - - -
229A GLU* 3.2 26.5 + - - +
410A PHE* 4.7 1.1 - - - -
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Residues in contact with CYS 124 (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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85A LEU* 5.0 4.5 - - - +
123A SER* 1.3 80.7 + - - +
125A SER* 1.3 61.8 + - - +
128A GLU 3.3 5.8 - - - +
129A CYS* 2.1 47.3 - - - -
184A HIS* 3.8 13.0 + - - +
189A TRP* 4.0 5.5 - - - -
229A GLU* 4.2 4.1 + - - +
410A PHE* 4.0 14.8 - - - -
411A VAL 3.8 21.7 + - - +
412A HIS* 3.9 25.1 - - - +
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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