Contacts of the strand formed by residues 119 - 126 (chain K) in PDB entry 2I2X
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 LYS 119 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E LYS* 4.1 15.0 - - - +
30K LEU 3.3 8.5 - - - +
31K ASP* 3.1 52.0 + - + +
32K LEU* 3.8 16.8 - - + -
33K GLU* 6.4 0.2 - - - -
38K TYR* 3.5 28.9 - - + +
79K PRO* 3.0 22.6 + - + +
80K ALA* 3.2 6.6 - - + -
81K ILE 3.1 21.5 + - - -
113K HIS* 4.6 0.4 - - - -
117K GLY 3.4 5.1 + - - +
118K ILE* 1.3 75.2 - - - +
120K CYS* 1.3 61.9 + - - +
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Residues in contact with CYS 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K LEU* 2.7 65.9 + - - +
32K LEU* 4.0 7.5 - - - +
70K MET* 4.0 21.3 - - + -
81K ILE* 3.0 28.0 - - + +
83K LEU* 5.3 0.4 - - + -
106K LYS* 6.2 0.2 - - - -
109K MET* 4.0 20.9 - - - -
113K HIS* 4.8 0.7 - - - -
118K ILE 3.6 6.5 + - - -
119K LYS* 1.3 74.8 - - - +
121K ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K ALA* 4.5 5.8 - - + -
29K GLY* 4.1 13.2 - - - +
32K LEU* 3.5 22.2 - - + +
81K ILE 3.3 5.1 + - - +
82K ILE* 3.3 11.2 - - + +
83K LEU* 3.1 23.4 + - - +
106K LYS* 5.6 0.9 - - - +
109K MET* 4.5 7.7 - - - +
120K CYS* 1.3 77.7 - - - +
122K LEU* 1.3 61.1 + - - +
159K ASP* 3.5 15.9 - - + +
160K LEU* 5.0 6.7 - - + -
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Residues in contact with LEU 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K ILE* 4.9 0.2 - - - -
83K LEU 3.4 17.7 - - - +
85K THR* 3.9 3.6 - - - +
102K ALA* 3.6 23.8 - - - +
105K GLN* 3.9 15.3 - - + +
106K LYS* 4.4 3.8 - - + +
109K MET* 3.6 33.8 - - + -
121K ALA* 1.3 74.7 - - - +
123K ARG* 1.3 63.1 + - - +
124K HIS* 3.8 29.8 - - + +
157K GLY 3.8 18.6 - - - +
158K ALA* 3.8 2.4 - - - -
159K ASP* 2.8 44.1 + - - +
160K LEU* 3.0 8.8 + - - -
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Residues in contact with ARG 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K GLU* 2.9 43.2 + - - +
82K ILE* 4.5 1.1 - - + -
83K LEU 2.8 12.9 + - - +
84K GLU* 3.4 20.8 + - + -
85K THR 2.7 32.7 + - - +
121K ALA 4.3 0.2 - - - -
122K LEU* 1.3 74.1 - - - +
124K HIS* 1.3 66.2 + - - +
125K THR* 3.9 8.3 - - - +
160K LEU* 3.5 28.1 - - + +
162K SER* 3.1 27.2 + - - +
215K ALA* 3.6 8.0 - - - +
216K GLY 4.5 0.2 - - - +
265K PRO* 2.6 37.3 + - - +
266K GLY* 3.5 14.4 + - - -
267K LYS* 3.7 9.7 - - - +
285K THR* 3.4 11.7 + - - -
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Residues in contact with HIS 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K THR* 3.4 14.5 - - - +
87K HIS* 3.1 31.4 - + - +
98K GLY 3.5 8.6 + - - -
101K VAL* 4.1 3.0 - - - +
102K ALA* 3.4 27.3 + - + +
105K GLN* 3.2 30.6 + - - -
122K LEU* 3.8 12.3 + - + +
123K ARG* 1.3 80.4 + - - +
125K THR* 1.3 61.8 + - - +
126K ILE* 3.7 13.7 - - + +
153K CYS* 3.7 15.0 - - + -
158K ALA* 3.9 16.9 - - + +
160K LEU 3.1 10.3 + - - +
161K LEU* 3.7 1.0 - - + -
162K SER 3.1 23.7 + - - +
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Residues in contact with THR 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K GLU* 2.8 26.8 + - - +
85K THR 2.8 13.4 + - - -
86K GLU* 3.8 13.1 - - + +
87K HIS* 2.9 28.8 + - - +
123K ARG* 3.9 1.4 - - - +
124K HIS* 1.3 71.0 - - - +
126K ILE* 1.3 63.6 - - - +
127K GLY* 3.5 0.5 + - - -
162K SER* 3.3 24.9 - - - +
163K VAL* 3.9 15.3 - - - -
164K GLU* 4.2 8.1 - - + -
267K LYS* 3.9 20.2 - - - -
500L B13 5.7 1.3 - - - +
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Residues in contact with ILE 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K HIS* 4.0 13.0 - - + -
92K SER* 3.5 13.2 - - - +
124K HIS* 3.7 27.6 - - + +
125K THR* 1.3 73.9 - - - +
127K GLY* 1.3 74.0 + - - +
146K PHE* 4.1 8.1 - - + -
149K ALA* 3.8 29.4 - - + +
150K PHE* 3.6 57.4 - - + +
153K CYS* 4.7 1.8 - - - -
161K LEU* 4.7 5.6 - - + -
162K SER 3.0 2.8 + - - -
163K VAL* 3.3 22.5 - - - +
164K GLU 4.5 0.7 + - - -
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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