Contacts of the strand formed by residues 123 - 128 (chain B) in PDB entry 3KHU
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 TYR 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B PHE* 3.8 50.8 - + + +
82B ALA 4.6 1.4 - - - +
83B ASP* 4.6 6.8 - - - +
121B ASN 3.6 1.5 + - - +
122B GLY* 1.3 70.9 - - - -
124B LYS* 1.3 73.5 + - - +
125B ILE* 3.7 28.5 - - + +
153B ASN* 3.4 29.2 - - + -
155B GLN* 3.8 19.2 - - + +
187B GLU* 3.7 21.4 + - - -
190B ARG* 4.7 4.7 - - - +
191B ALA* 3.9 13.0 + - - +
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Residues in contact with LYS 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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79B ILE 3.2 18.4 + - - +
80B LYS 2.9 23.1 + - - -
81B GLU 4.3 0.4 - - - -
82B ALA 2.6 28.1 + - - +
83B ASP 3.4 10.5 - - - +
85B VAL* 4.3 12.6 - - + -
116B ILE* 5.3 0.7 - - + -
120B SER* 3.4 35.9 - - - +
121B ASN 4.2 14.1 + - - +
122B GLY 4.0 0.8 + - - -
123B TYR* 1.3 83.4 + - - +
125B ILE* 1.3 68.2 + - - +
126B VAL* 5.0 2.2 - - + -
153B ASN 3.2 6.5 + - - +
154B LEU* 3.3 20.6 - - + +
155B GLN* 2.9 26.2 + - - +
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Residues in contact with ILE 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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2B PHE* 4.1 15.0 - - + -
4B ILE* 4.1 10.5 - - + -
83B ASP 3.0 6.8 + - - +
84B LEU* 3.2 23.8 - - + +
85B VAL* 2.8 32.2 + - - +
123B TYR* 3.7 27.6 - - + +
124B LYS* 1.3 74.7 - - - +
126B VAL* 1.3 56.1 + - - +
127B THR* 3.7 2.2 - - - +
155B GLN* 3.5 5.8 - - + +
157B LEU* 3.6 30.7 - - + -
191B ALA* 4.0 14.1 - - + +
194B ALA* 3.8 30.1 - - + -
195B LEU* 5.7 0.4 - - + -
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Residues in contact with VAL 126 (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 VAL* 3.3 14.4 - - + +
87B ILE* 3.7 28.3 - - + -
116B ILE* 3.9 25.8 - - + -
124B LYS* 4.9 0.9 - - + -
125B ILE* 1.3 74.6 - - - +
127B THR* 1.3 64.7 + - - +
128B GLU 4.3 0.2 - - - -
140B ILE* 4.7 5.8 - - + -
144B PHE* 3.9 32.5 - - + -
154B LEU* 4.4 14.1 - - + -
155B GLN 2.6 13.4 + - - +
156B VAL* 3.2 7.1 - - + +
157B LEU 2.9 24.8 + - - +
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Residues in contact with THR 127 (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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84B LEU* 3.2 22.8 - - - +
85B VAL 2.9 9.7 + - - -
86B PHE* 3.3 26.5 - - + -
87B ILE* 2.8 32.0 + - - -
125B ILE* 3.7 1.9 - - - +
126B VAL* 1.3 75.2 + - - +
128B GLU* 1.3 62.3 + - - +
129B LYS 3.4 0.7 + - - -
157B LEU* 3.3 19.6 - - + +
159B ASN* 3.4 36.6 - - + +
195B LEU* 4.1 6.6 - - + +
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Residues in contact with GLU 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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87B ILE* 3.9 10.7 - - + +
109B ILE* 5.8 2.0 - - + -
126B VAL* 4.3 0.8 + - - +
127B THR* 1.3 70.5 - - - +
129B LYS* 1.3 59.8 + - - +
130B SER 4.5 1.7 - - - +
132B VAL* 3.5 27.1 - - + +
136B ALA* 3.0 16.1 - - - +
137B ALA* 3.0 31.5 + - + +
140B ILE* 3.7 21.8 - - + +
156B VAL* 5.1 1.3 - - + -
157B LEU 3.0 12.2 + - - +
158B SER* 3.6 11.4 + - - -
159B ASN* 2.8 29.5 + - - +
160B PRO* 4.3 0.7 - - - +
217B GLU* 2.8 25.2 - - - +
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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