Contacts of the strand formed by residues 85 - 92 (chain G) in PDB entry 3KDO
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 TRP 85 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G ARG* 3.3 2.4 - - - -
31G VAL* 2.5 43.1 + - - +
33G PRO* 4.5 5.4 - - + +
39G ILE* 3.3 54.6 - - + +
77G PHE* 4.1 17.9 - - + -
78G HIS* 3.3 13.2 - - - -
79G ASP* 3.0 58.3 + - + -
80G MET* 4.6 0.4 - - - -
83G GLY* 4.5 7.6 + - - -
84G SER* 1.3 82.6 - - - +
86G ILE* 1.3 63.1 + - - +
87G VAL* 3.7 5.9 + - + -
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Residues in contact with ILE 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G VAL* 3.9 19.5 - - + -
29G PHE 3.3 1.3 - - - +
30G ARG* 3.9 25.4 - - + +
76G ASP* 3.6 5.6 - - - +
77G PHE* 3.6 1.0 - - - -
78G HIS* 2.8 46.5 + - + +
80G MET* 3.5 25.6 - - + -
85G TRP* 1.3 71.6 - - - +
87G VAL* 1.3 63.0 + - - +
88G ARG* 4.2 7.5 + - + +
124G GLU* 4.6 1.6 - - + +
349G VAL* 3.3 27.8 - - + +
350G PHE* 3.5 33.9 - - + -
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Residues in contact with VAL 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ALA 3.6 2.1 - - - +
28G VAL* 4.7 0.2 - - - -
29G PHE* 2.7 42.0 + - + +
31G VAL* 3.9 23.3 - - + -
39G ILE* 4.0 13.9 - - + -
43G ALA* 4.0 19.5 - - + -
74G ALA* 4.2 7.4 - - + -
76G ASP 3.2 9.6 - - - +
77G PHE* 3.9 23.3 - - + -
85G TRP* 4.2 4.0 - - + -
86G ILE* 1.3 78.3 - - - +
88G ARG* 1.3 71.1 + - - +
89G ILE* 3.9 15.0 + - + +
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Residues in contact with ARG 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ILE* 4.2 3.6 - - + -
27G ALA 3.4 5.2 - - - -
28G VAL* 4.5 17.4 - - + +
74G ALA* 3.8 0.5 - - - -
75G TYR* 3.2 56.2 + - + +
76G ASP* 3.1 42.4 + - + +
86G ILE* 5.2 5.3 - - + +
87G VAL* 1.3 76.2 - - - +
89G ILE* 1.3 62.9 + - - +
348G ASP 5.4 5.1 + - - -
349G VAL* 5.1 13.3 + - - +
351G HIS 5.7 1.2 + - - -
352G LEU* 4.0 28.2 - - - +
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Residues in contact with ILE 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ILE 3.5 1.0 - - - +
26G ILE* 3.2 5.4 - - - -
27G ALA* 2.9 36.2 + - + +
29G PHE* 4.1 11.0 - - + -
43G ALA 4.3 6.1 - - - +
46G VAL* 3.9 28.3 - - + -
47G ALA* 4.0 19.1 - - + +
72G ALA* 4.0 10.5 - - + -
73G LYS 3.3 16.4 - - - +
74G ALA* 4.0 9.4 - - + -
75G TYR* 3.8 2.7 - - - -
87G VAL* 4.0 14.4 - - + +
88G ARG* 1.3 80.1 - - - +
90G ALA* 1.3 62.8 + - - +
91G TYR* 3.6 29.1 - - + +
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Residues in contact with ALA 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G TYR* 3.7 30.5 - - + -
19G PRO* 4.3 4.9 - - + -
24G ASP* 4.2 12.8 - - + -
25G ILE 3.3 4.9 - - - +
26G ILE* 4.6 1.1 - - + +
71G SER 4.5 0.2 - - - +
72G ALA* 3.2 8.0 - - - +
73G LYS* 2.9 32.5 + - - +
75G TYR* 3.8 16.1 - - + -
89G ILE* 1.3 74.3 - - - +
91G TYR* 1.3 62.0 + - - +
92G PRO* 4.3 1.8 - - - +
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Residues in contact with TYR 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ASP* 3.2 5.7 - - - -
25G ILE* 2.4 58.7 + - + +
27G ALA* 3.8 9.6 - - + -
29G PHE* 4.3 9.7 - - - -
50G SER* 2.5 43.9 + - - -
51G SER* 4.4 4.9 - - - -
70G LEU 5.8 0.4 - - - -
72G ALA* 3.3 25.1 - - + -
89G ILE* 3.6 33.7 - - + +
90G ALA* 1.3 74.9 - - - +
92G PRO* 1.3 68.6 - - + +
96G PHE* 3.7 33.7 - + + -
108G ILE* 3.6 23.3 - - + +
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Residues in contact with PRO 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ARG* 3.7 23.1 - - - +
23G ARG* 3.6 8.1 - - + +
24G ASP* 3.8 7.4 - - - +
69G ASP 3.7 19.5 - - - +
70G LEU* 4.0 18.8 - - - +
71G SER 3.9 16.6 - - - +
72G ALA* 5.0 0.2 - - - -
90G ALA 4.3 1.3 - - - +
91G TYR* 1.3 86.3 - - + +
93G PHE* 1.3 67.2 + - - +
94G HIS* 3.8 14.1 - - + +
95G ALA* 2.9 25.1 + - + +
96G PHE* 4.0 2.9 - - - -
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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