Contacts of the strand formed by residues 55 - 62 (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 VAL 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PRO* 4.5 3.1 - - + -
54B ARG* 1.3 79.0 - - - +
56B ARG* 1.3 60.3 + - - +
57B CYS* 4.1 9.4 - - - -
124B ALA* 3.1 4.8 - - - -
125B PHE* 2.8 63.6 + - + -
138B SER* 4.4 4.5 - - - -
139B PHE* 3.7 37.9 - - + -
161B ARG* 3.7 30.7 - - - +
163B GLU 3.4 10.1 - - - +
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Residues in contact with ARG 56 (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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51A GLU 5.7 4.4 - - - +
55B VAL* 1.3 73.5 - - - +
57B CYS* 1.3 69.4 + - - +
121B ASP* 2.8 33.5 + - - +
123B GLY* 3.4 29.5 - - - -
124B ALA* 3.7 7.2 - - + +
161B ARG* 3.4 0.5 - - - -
162B THR* 2.9 39.9 + - - +
163B GLU* 2.9 51.8 + - + +
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Residues in contact with CYS 57 (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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55B VAL* 4.1 5.4 - - - -
56B ARG* 1.3 86.6 - - - +
58B SER* 1.3 64.3 + - - +
121B ASP* 3.9 3.5 - - - +
122B LEU* 3.1 33.4 + - + +
123B GLY 3.7 5.3 + - - -
125B PHE* 3.8 18.1 - - + -
138B SER* 3.7 31.9 - - - +
159B ILE* 3.8 19.3 - - + -
160B LEU 3.2 6.5 - - - +
161B ARG* 3.9 15.5 - - - -
162B THR* 4.0 3.6 - - - -
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Residues in contact with SER 58 (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* 1.3 77.1 - - - +
59B HIS* 1.3 64.6 + - - +
103B PHE* 3.7 20.0 - - - -
104B GLU* 5.9 2.2 - - - +
119B ARG 4.4 5.2 + - - -
120B GLY 3.2 13.9 - - - -
121B ASP* 3.5 20.1 + - - +
122B LEU* 4.8 0.4 - - - -
159B ILE* 3.5 3.8 - - - +
160B LEU* 2.6 35.5 + - - +
162B THR* 4.0 15.8 - - - +
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Residues in contact with HIS 59 (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 3.3 28.3 - + - -
58B SER* 1.3 77.0 - - - +
60B LEU* 1.3 58.0 + - - +
61B LEU* 3.8 17.9 - - + +
103B PHE* 3.6 7.0 - - - -
107B ALA* 3.7 6.6 - - - +
111B SER* 4.2 2.1 + - - -
113B CYS* 3.3 27.0 - - + +
115B SER* 3.4 13.4 + - - -
120B GLY* 3.1 23.8 + - - -
122B LEU* 3.7 17.3 - - + +
134B PHE* 3.7 18.6 - - + -
157B HIS* 3.1 25.7 + - + -
158B ILE 3.0 14.8 - - - +
159B ILE* 4.3 0.9 - - + -
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Residues in contact with LEU 60 (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* 1.3 74.1 - - - +
61B LEU* 1.3 65.6 + - - +
62B VAL* 3.7 26.7 - - + -
89B ILE* 3.9 5.3 - - + +
92B TYR* 3.8 29.8 - - + -
96B ILE* 5.6 2.0 - - + -
103B PHE* 3.7 10.3 - - + +
106B LEU* 3.7 40.8 - - + +
107B ALA* 3.8 6.1 - - + +
110B PHE* 4.4 1.6 - - + +
111B SER* 3.8 19.7 - - - -
157B HIS* 3.3 4.3 - - - -
158B ILE* 2.8 42.6 + - + +
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Residues in contact with LEU 61 (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 3.5 31.2 - - + -
59B HIS* 3.8 13.2 + - + -
60B LEU* 1.3 73.3 - - - +
62B VAL* 1.3 67.6 + - - +
63B LYS* 3.8 20.9 - - + -
110B PHE 3.9 0.5 - - - +
111B SER* 3.0 18.3 + - - +
112B ASP* 2.8 47.3 + - - +
113B CYS* 4.2 2.5 - - + -
154B SER* 4.0 4.0 - - - +
155B GLY* 3.9 20.0 - - - -
156B ILE 3.6 7.2 - - - +
157B HIS* 3.6 27.1 - - + +
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Residues in contact with VAL 62 (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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60B LEU* 3.7 11.9 - - + -
61B LEU* 1.3 77.4 - - - +
63B LYS* 1.3 66.8 + - - +
80B ARG* 3.6 32.1 - - - +
85B ALA* 3.8 18.7 - - + +
88B LEU* 3.9 9.9 - - + -
89B ILE* 3.6 31.6 - - + -
92B TYR* 3.9 16.8 - - + -
110B PHE 4.9 3.6 - - - +
112B ASP* 3.8 2.9 - - - +
155B GLY* 3.7 0.2 - - - -
156B ILE* 2.8 32.1 + - - -
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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