Contacts of the strand formed by residues 124 - 133 (chain B) in PDB entry 5H4Z
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 GLN 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B TYR* 3.4 9.9 + - - -
119B ASP* 2.8 34.3 + - - +
122B SER* 3.1 34.7 + - - +
123B GLY* 1.3 78.5 - - - +
125B LEU* 1.3 59.5 + - - +
126B LEU* 3.9 13.8 - - + +
178B ALA* 3.9 21.3 - - + +
179B PHE 3.3 17.7 - - - +
180B LYS* 3.6 23.5 + - - +
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Residues in contact with LEU 125 (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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116B LEU* 5.0 4.0 - - + -
117B ASP 3.7 27.8 - - - +
118B TYR* 3.9 18.3 - - + +
124B GLN* 1.3 71.7 - - - +
126B LEU* 1.3 61.7 + - - +
127B VAL* 3.8 17.9 + - + -
152B LEU* 4.5 21.8 - - + -
177B PHE 3.3 6.2 - - - +
178B ALA* 3.4 1.2 - - - -
179B PHE* 3.0 41.7 + - + +
186B LEU* 4.9 9.4 - - + -
191B LEU* 5.2 3.1 - - + -
214B MET* 4.1 37.9 - - + -
219B LEU* 4.5 7.4 - - + -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER* 3.7 1.6 + - - +
116B LEU* 3.6 5.0 + - - -
117B ASP* 2.7 55.8 + - + +
119B ASP* 3.8 28.0 - - + +
124B GLN* 3.9 29.8 - - + +
125B LEU* 1.3 79.1 - - - +
127B VAL* 1.3 61.3 + - - +
128B GLY 3.8 1.4 + - - -
176B THR* 4.4 16.6 - - + -
177B PHE 3.4 2.5 - - - -
178B ALA* 4.1 13.7 - - + -
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER 3.5 7.9 - - - +
116B LEU* 4.2 4.3 - - + -
125B LEU* 4.1 13.9 - - + -
126B LEU* 1.3 74.3 - - - +
128B GLY* 1.3 61.5 + - - +
129B ILE* 3.5 22.6 + - + -
150B VAL* 4.2 11.0 - - + -
176B THR* 3.5 3.4 - - - +
177B PHE* 2.8 38.6 + - + +
179B PHE* 3.9 30.5 - - + -
191B LEU* 3.9 32.5 - - + -
193B MET* 4.4 2.5 - - - -
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Residues in contact with GLY 128 (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 TYR* 3.1 9.4 - - - +
115B SER* 2.7 52.0 + - - +
126B LEU 3.8 2.2 + - - -
127B VAL* 1.3 70.6 - - - +
129B ILE* 1.3 62.1 + - - +
130B LEU* 3.7 8.9 + - - +
175B GLU 3.5 7.9 - - - -
176B THR* 4.1 10.9 - - - +
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Residues in contact with ILE 129 (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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112B LEU* 4.4 10.8 - - + -
113B GLN 4.4 1.8 - - - -
114B TYR* 4.4 2.7 - - + -
127B VAL* 4.0 10.5 - - + +
128B GLY* 1.3 75.1 - - - +
130B LEU* 1.3 59.9 + - - +
148B VAL* 4.1 17.3 - - + -
150B VAL* 4.0 19.5 - - + -
162B THR* 4.4 6.5 - - + -
173B PHE* 3.3 31.9 - - + +
174B GLY* 3.1 19.6 + - - -
175B GLU 2.8 18.7 + - - +
177B PHE* 4.0 16.2 - - + -
193B MET* 3.7 36.3 - - + -
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Residues in contact with LEU 130 (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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113B GLN* 3.1 44.2 + - + +
114B TYR 3.9 15.3 - - - -
115B SER* 4.1 6.1 - - - +
128B GLY* 3.7 17.9 + - - +
129B ILE* 1.3 78.8 - - - +
131B GLN* 1.3 59.8 + - + +
172B HIS* 3.6 1.9 + - - +
173B PHE* 2.7 30.4 + - - -
174B GLY* 3.0 14.2 + - - +
175B GLU 5.1 0.9 - - - +
176B THR* 6.1 0.2 - - - +
224B GLN* 3.9 28.3 - - - +
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Residues in contact with GLN 131 (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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112B LEU* 3.7 6.8 - - - +
113B GLN* 2.8 61.9 + - + +
130B LEU* 1.3 81.8 - - - +
132B ALA* 1.3 60.8 + - - +
133B MET* 4.2 15.6 - - - +
170B ASN 6.0 0.2 - - - -
171B PRO 3.2 14.1 - - - +
172B HIS* 3.2 35.2 + - - +
173B PHE* 4.1 6.2 - - - -
226B TRP* 3.5 23.6 - - + -
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Residues in contact with ALA 132 (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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111B GLN 3.4 11.0 - - - +
112B LEU* 4.4 13.5 - - + -
131B GLN* 1.3 79.7 - - - +
133B MET* 1.3 64.9 + - - +
135B LEU* 4.1 19.3 - - + -
170B ASN* 3.4 13.3 - - - -
171B PRO* 3.0 37.0 + - + +
173B PHE* 4.3 5.7 - - + -
195B VAL* 5.5 4.5 - - + -
226B TRP* 4.9 0.9 - - - -
229B LEU* 6.0 0.2 - - + -
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Residues in contact with MET 133 (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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110B GLY* 3.8 0.3 - - - -
111B GLN* 3.0 47.0 + - - +
131B GLN* 4.2 17.7 - - - +
132B ALA* 1.3 77.1 - - - +
134B GLY* 1.3 64.7 + - - +
135B LEU* 3.5 2.0 + - - -
169B LEU 3.9 2.0 + - - -
170B ASN* 3.0 26.0 - - + +
172B HIS* 5.5 4.9 - - + +
226B TRP* 4.1 28.3 - - + -
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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