Contacts of the strand formed by residues 44 - 55 (chain X) in PDB entry 3FKS
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 44 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39X ILE 4.2 0.2 - - - +
40X LYS* 4.7 1.7 - - - -
41X THR* 2.8 31.9 + - - +
42X PRO 3.4 0.4 - - - -
43X GLN* 1.3 82.0 - - - +
45X LYS* 1.3 65.0 + - - +
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Residues in contact with LYS 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X GLU* 3.3 42.1 + - + +
39X ILE 3.5 10.1 - - - +
40X LYS* 5.9 0.4 - - - -
41X THR* 3.5 1.6 - - - +
44X GLY* 1.3 76.9 - - - +
46X LEU* 1.3 60.6 + - - +
47X VAL* 3.0 19.2 + - + +
65X ASP* 4.9 4.3 - - - +
99X ILE* 3.9 27.1 - - - +
101X GLU* 4.2 16.5 + - - -
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Residues in contact with LEU 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X VAL* 5.6 0.4 - - + -
38X GLU* 3.6 1.6 - - - -
39X ILE* 3.1 46.5 + - + +
41X THR* 3.5 13.0 - - + +
45X LYS* 1.3 68.0 - - - +
47X VAL* 1.3 70.8 + - - +
48X LEU* 4.2 6.5 - - + +
63X ALA* 5.4 4.0 - - + -
65X ASP* 3.7 27.8 - - + +
66X GLY 3.1 29.2 - - - +
67X THR* 4.5 4.5 - - + -
68X GLU 6.1 0.2 - - - +
70X LEU* 3.8 35.9 - - + -
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Residues in contact with VAL 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X ALA* 6.0 2.2 - - + -
37X LEU 3.2 4.9 - - - +
38X GLU* 3.7 28.0 - - + +
45X LYS* 3.0 27.2 + - - +
46X LEU* 1.3 79.6 - - - +
48X LEU* 1.3 73.0 + - - +
63X ALA* 4.3 0.9 - - - -
64X MET* 3.9 37.9 + - + -
65X ASP* 4.8 9.5 + - - +
83X ILE* 5.7 4.7 - - + -
99X ILE* 4.1 29.8 - - + -
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Residues in contact with LEU 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X VAL* 3.9 32.3 - - + -
23X VAL* 4.6 4.7 - - + -
36X ALA* 3.2 10.7 - - - +
37X LEU* 2.7 54.5 + - + -
39X ILE* 4.3 23.1 - - + -
46X LEU* 4.2 8.7 - - + +
47X VAL* 1.3 82.8 - - - +
49X GLU* 1.3 62.6 + - - +
50X VAL 4.3 0.2 - - - -
61X THR* 3.3 26.9 - - - +
62X ILE 3.9 5.6 - - - +
63X ALA* 3.9 18.8 - - + -
64X MET* 4.1 4.7 - - - +
83X ILE* 4.3 3.5 - - - +
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Residues in contact with GLU 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X LEU* 3.9 20.3 - - - +
35X ASN 3.4 3.6 - - - -
48X LEU* 1.3 78.0 - - - +
50X VAL* 1.3 74.1 + - - +
51X ALA* 3.2 2.4 + - + +
61X THR* 3.8 3.3 - - - -
62X ILE* 3.1 36.8 + - + +
64X MET* 4.0 13.9 - - + +
83X ILE* 3.4 19.3 - - + +
117X ILE* 4.3 1.9 - - - +
118X HIS* 3.0 28.1 + - - -
231X ARG* 3.2 43.7 + - - +
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Residues in contact with VAL 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X PRO* 4.0 17.9 - - + +
32X ALA 3.4 27.4 - - - +
33X ILE* 3.5 1.8 - - - +
34X LEU* 2.9 30.0 + - - +
35X ASN 3.1 13.1 + - - +
37X LEU* 3.8 19.3 - - + -
48X LEU 4.3 0.2 - - - -
49X GLU* 1.3 72.6 - - - +
51X ALA* 1.3 60.7 - - - +
52X GLN 4.2 6.7 - - - +
53X HIS* 4.4 4.3 - - + -
59X VAL* 3.8 31.2 - - + -
60X ARG 4.1 1.6 - - - +
61X THR* 3.5 21.1 - - + +
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Residues in contact with ALA 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U GLY* 4.3 3.8 - - - -
38U ASP* 4.3 13.5 + - - +
33X ILE* 3.5 24.0 - - - +
49X GLU* 3.2 1.5 + - + +
50X VAL* 1.3 74.5 - - - +
52X GLN* 1.3 62.9 + - - +
60X ARG 2.8 11.5 + - - +
62X ILE* 4.1 29.4 - - + -
231X ARG* 5.8 4.9 - - - +
272X LEU* 4.6 13.5 - - + -
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Residues in contact with GLN 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U VAL 3.6 11.7 - - - +
37U GLY* 4.2 7.8 - - - -
38U ASP* 3.6 18.8 - - - +
33X ILE* 3.9 3.7 - - - +
50X VAL* 3.8 1.3 - - - +
51X ALA* 1.3 84.1 - - + +
53X HIS* 1.3 63.4 + - - +
54X LEU* 3.1 18.8 + - + +
59X VAL* 3.6 1.3 - - - -
60X ARG* 2.9 65.1 + - + +
272X LEU* 3.2 37.8 + - - +
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Residues in contact with HIS 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U ALA* 3.1 18.9 - - - +
36U VAL* 2.8 33.2 + - + +
84U VAL 5.3 0.4 + - - -
85U LYS* 4.4 6.2 - - + -
86U GLU* 3.4 43.0 + - + +
30X LEU* 3.8 25.6 - - + -
31X PRO 2.8 27.4 + - - -
32X ALA* 3.6 9.5 - - - -
33X ILE* 3.7 20.0 - - + -
50X VAL* 4.4 1.3 - - + -
52X GLN* 1.3 68.7 - - - +
54X LEU* 1.3 66.0 + - - +
55X GLY 3.1 2.5 + - - -
58X THR 4.0 4.9 - - - -
59X VAL* 3.7 13.6 - - + +
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Residues in contact with LEU 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U ALA* 3.2 15.9 - - - +
42U ARG* 4.6 6.6 + - - -
22X ASP* 3.5 32.3 - - + +
52X GLN* 3.1 38.4 + - + +
53X HIS* 1.3 71.0 - - - +
55X GLY* 1.3 58.8 + - - +
58X THR* 3.1 19.0 + - + +
59X VAL 4.3 2.9 - - - +
60X ARG* 3.5 39.5 - - + +
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Residues in contact with GLY 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U LEU 3.4 19.5 - - - -
35U ALA* 4.4 0.2 - - - -
86U GLU* 3.6 6.7 + - - -
53X HIS 3.1 2.4 + - - -
54X LEU* 1.3 80.4 - - - +
56X GLU* 1.3 73.7 + - - +
57X ASN 3.2 2.9 - - - -
58X THR* 2.9 23.4 + - - -
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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