Contacts of the strand formed by residues 115 - 124 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B SER* 5.8 0.3 - - - -
113B ASP 4.2 0.2 + - - -
114B VAL* 1.3 84.8 - - - +
116B VAL* 1.3 61.3 + - - +
117B ILE* 3.6 24.4 + - + +
133B PHE* 4.4 2.7 - + - -
135B THR* 3.8 24.5 - - + -
137B GLY* 5.3 1.3 - - - -
138B ALA 3.4 18.2 - - - -
139B LEU* 3.8 13.6 - - + +
140B LEU* 4.2 3.5 - - - +
159B MET* 3.9 28.7 - - + -
167B PRO* 2.9 27.8 + - + +
168B SER 3.5 24.5 - - - -
169B PRO* 3.7 19.3 - - + -
171B SER* 4.0 6.1 - - - -
440B SER* 4.1 2.8 + - - -
108C ILE* 3.7 27.1 - - + -
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Residues in contact with VAL 116 (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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114B VAL 3.5 1.0 + - - -
115B PHE* 1.3 72.7 - - - +
117B ILE* 1.3 63.9 + - - +
135B THR* 3.5 0.9 - - - -
136B GLN* 3.0 57.0 + - + -
138B ALA* 2.9 33.7 + - + +
139B LEU 4.1 2.0 - - - +
140B LEU* 4.4 8.7 - - + -
145B SER* 4.2 16.4 - - - +
148B THR* 3.8 8.1 - - + +
438B TRP* 5.7 0.2 - - + -
439B THR 3.2 27.8 - - - +
440B SER* 3.3 11.0 - - - +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASP* 5.7 3.1 - - - +
105B SER* 5.1 1.1 - - - +
115B PHE* 3.8 24.5 - - + +
116B VAL* 1.3 83.5 - - - +
118B ARG* 1.3 75.3 + - - +
120B PRO* 4.2 17.3 - - + -
131B THR* 6.5 0.2 - - + -
133B PHE* 3.9 37.0 - - + -
134B LEU 3.4 11.9 - - - +
135B THR* 4.1 2.0 - - - -
136B GLN* 5.1 1.3 - - - +
156B ARG* 4.5 1.6 - - - +
167B PRO* 4.4 18.2 - - + -
439B THR 4.2 1.2 - - - +
440B SER* 2.9 28.3 + - - +
441B GLY 3.3 31.5 + - - +
442B SER* 5.6 0.7 - - - -
443B SER* 6.4 0.4 - - - -
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 1.3 83.5 - - - +
119B GLU* 1.3 105.2 + - - +
120B PRO* 3.3 6.0 - - - +
133B PHE* 4.3 0.5 - - - -
134B LEU 3.3 20.3 + - - +
136B GLN* 5.6 1.6 - - + +
148B THR 5.5 3.8 - - - +
151B ASP* 5.6 1.0 + - - -
156B ARG* 3.4 9.2 - - - +
371B ARG* 4.7 0.6 - - - +
406B TYR* 3.4 29.3 - - - -
425B GLU* 2.6 41.6 + - - -
427B ILE* 3.5 25.4 - - - +
439B THR* 4.3 28.0 - - + +
440B SER 4.6 5.4 - - - -
441B GLY* 5.1 0.4 - - - +
801B G39 3.4 18.6 + - - +
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Residues in contact with GLU 119 (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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118B ARG* 1.3 101.5 + - - +
120B PRO* 1.3 66.0 - - - +
121B PHE* 3.9 11.6 - - - -
133B PHE* 3.9 9.5 - - - -
134B LEU* 3.7 17.3 + - + +
151B ASP* 5.0 0.2 - - - +
156B ARG* 2.9 35.0 + - - -
227B GLU* 4.1 29.2 - - + +
406B TYR* 4.3 22.0 - - + -
425B GLU* 2.8 15.2 + - - -
801B G39 3.1 30.0 + - - +
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Residues in contact with PRO 120 (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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117B ILE* 4.2 20.9 - - + -
118B ARG* 3.3 4.9 - - - +
119B GLU* 1.3 92.2 - - - +
121B PHE* 1.3 63.0 + - - +
131B THR* 4.8 8.5 - - + -
132B PHE 3.3 11.2 - - - +
133B PHE* 4.1 4.0 - - + -
227B GLU 4.2 0.2 - - - +
423B TRP* 3.0 31.7 - - + -
425B GLU* 3.1 39.3 - - + +
441B GLY 6.1 0.2 - - - -
442B SER 4.7 5.6 - - - +
443B SER* 4.7 11.2 - - - -
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Residues in contact with PHE 121 (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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119B GLU 3.9 8.7 - - - -
120B PRO* 1.3 79.3 - - - +
122B ILE* 1.3 69.0 + - - +
123B SER* 4.5 1.6 - - - -
130B ARG 4.0 0.3 - - - +
131B THR* 3.6 2.6 - - - +
132B PHE* 2.8 76.4 + + + -
133B PHE* 5.0 0.4 - - - -
134B LEU* 6.3 1.3 - - + -
158B LEU* 4.5 9.4 - - + -
180B ALA* 4.3 11.9 - - + -
181B SER* 4.0 7.6 - - - -
182B ALA* 4.0 26.7 - - + -
227B GLU* 3.6 24.9 - - - +
228B SER* 3.6 6.1 - - - -
229B GLU* 3.6 22.7 - - - -
423B TRP* 3.5 25.6 - - + +
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Residues in contact with ILE 122 (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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100B TYR* 5.0 1.1 - - + -
101B SER* 4.3 3.6 - - - +
121B PHE* 1.3 79.0 - - - +
123B SER* 1.3 71.6 + - - +
124B CYS* 4.4 4.7 - - - -
129B CYS* 4.6 0.4 - - + -
130B ARG 3.4 12.3 - - - +
131B THR* 4.2 9.9 - - + +
163B VAL* 3.8 27.4 - - + -
229B GLU* 3.7 6.8 + - - +
409B SER 4.6 0.3 - - - +
410B PHE* 2.9 57.7 - - + +
423B TRP* 3.5 16.6 + - + -
443B SER* 5.8 5.8 - - - +
444B ILE 5.6 0.2 - - - -
445B SER* 3.5 35.7 - - - +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 4.1 2.4 + - - -
122B ILE* 1.3 77.0 - - - +
124B CYS* 1.3 64.0 + - - +
130B ARG 3.1 25.7 + - - +
132B PHE* 4.2 10.7 - - - -
182B ALA 3.5 10.3 + - - -
183B CYS* 3.8 5.7 - - - -
184B HIS 4.6 0.3 + - - -
189B TRP* 3.4 28.4 - - - -
229B GLU* 2.9 35.0 + - - +
410B PHE* 4.6 0.9 - - - -
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Residues in contact with CYS 124 (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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85B LEU* 5.2 4.2 - - - +
122B ILE* 4.4 0.2 - - - -
123B SER* 1.3 79.3 + - - +
125B SER* 1.3 69.3 + - - +
128B GLU 3.4 4.5 - - - +
129B CYS* 2.1 48.2 - - - -
184B HIS* 3.9 12.8 + - - +
189B TRP* 4.1 5.2 - - - -
229B GLU* 3.9 3.9 + - - +
410B PHE* 4.1 17.3 - - - -
411B VAL 3.9 21.3 + - - +
412B HIS* 4.1 14.7 - - - +
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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