Contacts of the helix formed by residues 121 - 131 (chain B) in PDB entry 1KWZ
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 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B PRO* 1.3 70.5 - - - +
122B SER* 1.3 64.7 + - - +
124B VAL* 3.1 5.9 + - + +
125B LYS* 2.9 48.8 + - + +
135B VAL* 4.3 11.9 - - + -
156B PHE* 3.2 38.9 - + + -
157B LEU 3.3 26.5 - - - -
158B GLY* 4.4 0.9 - - - -
160B THR* 3.6 22.4 - - + -
162B GLU* 5.3 5.2 - - - -
171B VAL* 3.7 24.0 - - + -
195B CYS* 3.5 22.2 - - - -
209B CYS* 3.1 25.2 + - + +
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Residues in contact with SER 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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120B PRO* 4.1 11.9 - - - +
121B PHE* 1.3 79.9 - - - +
123B LYS* 1.3 63.9 + - - +
125B LYS* 3.6 7.7 + - - +
126B ALA* 3.1 26.7 + - - +
209B CYS 4.6 1.2 + - - -
210B GLN* 6.2 1.8 - - - -
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Residues in contact with LYS 123 (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 MET* 3.3 22.1 - - + +
120B PRO* 2.9 34.6 + - + +
122B SER* 1.3 86.2 + - - +
124B VAL* 1.3 61.0 + - - +
126B ALA* 3.8 5.6 - - - +
127B LEU* 2.8 32.6 + - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B MET* 3.4 26.9 - - + +
120B PRO 3.1 8.1 + - - +
121B PHE* 3.1 8.3 + - + +
123B LYS* 1.3 75.5 - - - +
125B LYS* 1.3 59.3 + - - +
127B LEU* 3.5 3.7 - - - +
128B CYS* 2.9 36.9 + - - -
135B VAL* 3.8 30.3 - - + -
156B PHE* 3.9 25.6 - - + -
213B HIS 4.4 0.4 - - - +
215B ALA* 3.8 31.2 - - + -
216B VAL 4.4 1.8 - - - +
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Residues in contact with LYS 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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121B PHE* 2.9 48.2 + - + +
122B SER* 3.7 7.6 - - - +
124B VAL* 1.3 77.8 - - - +
126B ALA* 1.3 61.6 + - - +
128B CYS* 4.4 0.5 - - - +
129B SER* 2.8 37.0 + - - -
135B VAL* 3.7 25.1 - - + +
171B VAL* 4.3 24.8 + - + +
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Residues in contact with ALA 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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122B SER 3.1 18.3 + - - +
123B LYS* 3.2 6.9 + - - +
125B LYS* 1.3 76.5 - - - +
127B LEU* 1.3 58.4 + - - +
129B SER* 3.4 6.3 + - - -
130B GLU* 2.9 30.7 + - - +
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Residues in contact with LEU 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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101A PHE* 3.7 33.0 - - + -
107A SER* 4.3 15.7 - - - +
115B ASN* 4.6 3.6 - - - +
119B MET* 3.7 28.7 - - + -
123B LYS 2.8 17.5 + - - +
124B VAL* 3.5 4.3 - - - +
126B ALA* 1.3 74.1 - - - +
128B CYS* 1.3 67.1 + - - +
130B GLU* 3.0 30.4 + - - +
131B LEU* 3.2 25.1 + - + +
215B ALA* 4.5 4.0 - - + -
217B CYS* 5.1 0.9 - - - -
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Residues in contact with CYS 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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124B VAL* 2.9 28.7 + - - +
125B LYS 4.4 1.8 - - - +
127B LEU* 1.3 73.2 - - - +
129B SER* 1.3 61.9 + - - +
131B LEU* 3.0 11.9 + - - +
133B GLY* 2.8 24.9 + - - -
134B THR* 3.6 27.1 - - - +
135B VAL* 4.0 6.1 - - + +
215B ALA* 5.6 0.7 - - - -
216B VAL 3.9 7.4 - - - -
217B CYS* 2.0 56.3 - - + -
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Residues in contact with SER 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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125B LYS* 2.8 30.0 + - - -
126B ALA* 3.5 6.5 - - - -
128B CYS* 1.3 76.8 - - - +
130B GLU* 1.3 59.0 + - - +
132B ARG* 3.0 24.1 + - - +
133B GLY 3.8 11.9 + - - -
134B THR* 5.7 1.9 - - - +
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Residues in contact with GLU 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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94A LEU* 3.4 20.3 - - - +
97A LYS* 3.5 35.2 + - + +
126B ALA* 2.9 16.4 + - - +
127B LEU* 3.0 23.6 + - - +
129B SER* 1.3 76.9 - - - +
131B LEU* 1.3 61.0 + - + +
132B ARG* 3.2 2.2 + - - +
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Residues in contact with LEU 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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94A LEU* 4.5 9.9 - - + +
97A LYS* 3.5 37.5 - - + +
98A LEU* 3.7 22.7 - - + +
101A PHE* 3.7 43.5 - - + -
127B LEU* 3.2 20.2 + - + +
128B CYS 3.0 8.2 + - - +
130B GLU* 1.3 81.5 - - + +
132B ARG* 1.3 72.3 + - - +
133B GLY 3.3 0.4 - - - -
217B CYS* 4.7 4.9 - - - -
219B PHE* 3.3 24.3 - - + -
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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