Contacts of the strand formed by residues 103 - 109 (chain B) in PDB entry 2KAI
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 LEU 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.5 23.8 - - + -
54A THR 3.6 4.3 - - - +
56A ALA* 3.4 8.6 - - - +
91A HIS* 2.9 34.7 + - + +
101B HIS* 3.2 3.8 + - - -
102B ASP* 1.3 82.5 - - - +
104B MET* 1.3 64.2 + - - +
212B ILE* 3.9 19.5 - - + -
229B THR* 4.1 13.5 - - + -
231B LEU* 4.3 3.1 - - + -
234B TYR* 3.3 44.2 - - + -
237B TRP* 3.6 27.4 - - + -
238B ILE* 4.5 4.5 - - + -
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Residues in contact with MET 104 (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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52A VAL 3.8 0.2 - - - +
53A LEU* 3.6 5.5 - - - +
54A THR* 2.8 52.7 + - + +
55A ALA 3.8 8.1 - - - +
56A ALA* 3.6 14.6 - - - +
58A CYS 4.2 3.1 - - - +
59A LYS* 3.7 31.9 - - - +
63A TYR* 3.6 18.8 - - + +
88A ASP* 3.8 11.2 - - - +
89A PHE 3.6 5.8 - - - +
90A PRO* 3.6 22.4 - - + -
103B LEU* 1.3 79.1 - - - +
105B LEU* 1.3 66.4 + - - +
106B LEU* 3.4 23.6 - - + -
237B TRP* 4.3 1.1 - - - -
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Residues in contact with LEU 105 (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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47A VAL* 4.0 23.1 - - + -
51A TRP* 3.7 30.5 - - + -
52A VAL 3.3 16.6 - - - +
53A LEU* 4.0 10.3 - - + -
88A ASP* 3.3 1.0 - - - -
89A PHE* 2.8 46.9 + - + +
104B MET* 1.3 73.7 - - - +
106B LEU* 1.3 64.4 + - - +
107B ARG 4.1 0.4 - - - -
237B TRP* 4.0 14.3 - - + -
238B ILE* 4.1 10.3 - - + +
241B THR* 3.4 31.6 - - + -
242B ILE* 4.0 13.2 - - + -
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Residues in contact with LEU 106 (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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33A ILE* 3.5 32.1 - - + -
51A TRP* 3.4 5.3 - - - -
52A VAL* 2.9 46.2 + - + +
54A THR* 4.0 8.7 - - + -
63A TYR* 4.1 20.0 - - + -
65A VAL* 4.2 11.4 - - + -
85A VAL* 3.9 18.2 - - + -
87A ALA 3.7 2.7 - - - -
88A ASP* 3.7 15.0 - - + -
104B MET* 3.4 26.5 - - + -
105B LEU* 1.3 80.0 - - - +
107B ARG* 1.3 61.7 + - - +
108B LEU* 3.3 2.8 + - + -
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Residues in contact with ARG 107 (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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50A LYS* 3.4 23.6 - - + +
51A TRP* 3.7 30.1 - - + -
85A VAL* 3.2 3.2 - - - +
86A THR* 2.9 66.9 + - - +
87A ALA* 2.9 32.1 + - - +
89A PHE* 3.5 24.2 - - + -
106B LEU* 1.3 69.0 - - - +
108B LEU* 1.3 65.8 + - - +
245B ASN* 4.1 2.4 - - - +
246B PRO* 3.1 55.5 + - - +
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Residues in contact with LEU 108 (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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46A LEU* 4.0 20.2 - - + -
49A PRO 3.6 19.5 - - - +
50A LYS* 2.6 37.4 + - - +
52A VAL* 3.7 14.8 - - + -
65A VAL* 3.6 34.8 - - + -
67A LEU* 4.2 5.8 - - + -
83A PHE* 3.9 30.1 - - + -
84A GLY 3.6 5.6 - - - +
85A VAL* 4.4 2.7 - - + -
86A THR* 3.7 4.7 - - - +
106B LEU 3.3 2.5 + - - +
107B ARG* 1.3 74.2 - - - +
109B GLN* 1.3 66.7 + - - +
110B SER 3.1 14.4 + - - +
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Residues in contact with GLN 109 (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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50A LYS* 4.4 6.9 - - - -
83A PHE* 4.0 6.4 - - + -
84A GLY* 2.8 43.5 + - - +
85A VAL 5.5 0.2 - - - -
86A THR* 3.8 17.6 - - - +
107B ARG 3.5 2.2 + - - -
108B LEU* 1.3 71.3 - - - +
110B SER* 1.3 64.6 + - - +
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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