Contacts of the strand formed by residues 155 - 163 (chain B) in PDB entry 3IKG
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 GLY 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B LEU* 3.9 6.3 - - - +
62B VAL 3.7 8.3 - - - -
64B HIS* 4.0 12.5 + - - -
67B SER* 3.7 9.0 - - - -
151B PHE* 3.8 1.7 - - - -
152B THR* 3.0 34.3 + - - +
153B ASP 3.5 0.2 - - - -
154B SER* 1.3 80.4 - - - +
156B ILE* 1.3 65.6 + - - +
157B HIS* 3.7 1.4 - - - -
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.6 0.5 - - - -
62B VAL 2.8 37.9 + - - +
64B HIS* 4.6 1.8 - - + +
82B GLN* 4.4 16.4 - - + +
85B ALA* 4.4 13.9 - - + -
86B LEU* 4.2 11.0 - - + +
89B ILE* 3.5 29.1 - - + +
149B PRO* 4.0 24.7 - - + -
150B VAL 3.4 7.9 - - - +
151B PHE* 3.9 26.2 - - + -
155B GLY* 1.3 76.2 - - - -
157B HIS* 1.3 65.1 + - - +
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Residues in contact with HIS 157 (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 J8Z 3.6 34.3 - + - -
59B HIS* 3.1 24.8 + - - +
60B LEU 3.3 8.7 - - - +
61B LEU* 3.6 19.8 - - + +
89B ILE* 4.2 2.7 - - - -
134B PHE* 3.7 9.6 - + - -
148B GLY 3.5 0.9 - - - +
149B PRO* 3.4 5.8 - - - +
150B VAL* 2.6 56.2 + - + +
152B THR* 2.6 36.9 + - + +
154B SER* 4.4 0.2 - - - -
155B GLY 3.7 2.9 + - - -
156B ILE* 1.3 78.5 - - - +
158B ILE* 1.3 64.3 + - - +
159B ILE* 4.1 12.3 - - + -
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Residues in contact with ILE 158 (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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59B HIS* 3.0 6.1 - - - +
60B LEU* 2.8 45.2 + - + +
89B ILE* 3.7 32.8 - - + +
92B TYR* 4.0 16.4 - - + -
93B ILE* 3.4 32.8 - - + +
96B ILE* 4.6 6.7 - - + -
103B PHE* 3.5 22.8 - - + -
146B MET* 3.6 26.2 - - + -
147B SER* 3.8 10.8 - - - +
148B GLY 4.6 0.2 - - - -
157B HIS* 1.3 72.9 - - - +
159B ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 159 (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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57B CYS* 3.8 26.9 - - + -
58B SER 3.5 9.6 - - - +
59B HIS* 4.4 0.4 - - + -
103B PHE* 4.6 0.4 - - - -
134B PHE* 3.5 39.7 - - + +
137B ALA* 3.9 28.7 - - + -
138B SER* 3.9 11.0 - - - +
141B LEU* 3.9 14.9 - - + +
145B GLU 3.8 0.9 - - - +
146B MET* 3.3 6.2 - - - +
147B SER* 2.8 40.7 + - - +
150B VAL* 3.9 12.8 - - + -
157B HIS* 4.3 5.8 - - + -
158B ILE* 1.3 77.4 - - - +
160B LEU* 1.3 63.6 + - - +
161B ARG 4.2 0.2 - - - -
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Residues in contact with LEU 160 (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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57B CYS* 3.2 2.5 - - - -
58B SER* 2.6 45.7 + - - +
103B PHE* 4.1 32.9 - - + -
104B GLU* 4.1 18.8 - - - +
144B GLY* 3.9 20.0 - - - +
145B GLU 3.6 17.9 - - - +
146B MET* 4.1 11.7 - - + -
159B ILE* 1.3 76.2 - - - +
161B ARG* 1.3 65.5 + - - +
162B THR* 3.5 19.8 + - + +
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Residues in contact with ARG 161 (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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52B PRO* 3.8 19.4 - - - +
55B VAL* 3.7 21.5 - - - +
56B ARG 3.4 8.1 - - - +
57B CYS* 3.9 10.3 - - - -
138B SER 4.1 9.2 - - - +
139B PHE 4.4 7.1 + - - -
141B LEU* 2.9 40.5 + - + +
142B ARG* 3.8 16.6 - - - +
143B THR* 3.5 19.5 + - - +
144B GLY* 2.7 33.8 + - - -
145B GLU 3.2 7.7 + - - -
159B ILE 4.2 0.6 - - - -
160B LEU* 1.3 72.2 - - - +
162B THR* 1.3 58.0 + - - +
163B GLU* 2.8 43.7 + - - +
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Residues in contact with THR 162 (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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56B ARG* 2.9 36.9 + - - +
57B CYS* 3.8 1.7 + - - -
58B SER* 4.0 14.1 - - - +
143B THR* 3.4 14.0 - - - +
144B GLY* 4.7 1.1 - - - +
160B LEU* 3.5 29.3 + - + +
161B ARG* 1.3 76.4 - - - +
163B GLU* 1.3 70.9 + - - +
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Residues in contact with GLU 163 (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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52B PRO* 6.0 0.3 - - - +
54B ARG 5.0 2.4 - - - +
55B VAL* 3.4 5.8 - - - -
56B ARG* 2.9 64.0 + - + +
124B ALA* 5.4 3.8 - - - +
143B THR* 3.5 11.8 + - - +
161B ARG* 2.8 44.7 + - - +
162B THR* 1.3 89.6 + - - +
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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