Contacts of the helix formed by residues 27 - 46 (chain x) in PDB entry 6FF7
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 THR 27 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25x ASP 3.4 4.7 + - - -
26x THR* 1.3 80.0 - - - +
28x LYS* 1.3 65.6 + - - +
29x TRP* 3.5 5.2 - - - -
30x GLU* 3.8 16.6 + - - +
31x TRP* 3.8 11.3 + - - +
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Residues in contact with LYS 28 (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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4848 ASP* 5.3 13.2 - - + -
27x THR* 1.3 73.4 - - - +
29x TRP* 1.3 61.6 + - - +
31x TRP* 3.5 3.7 + - - +
32x LEU* 3.0 29.5 + - - +
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Residues in contact with TRP 29 (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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27x THR* 3.5 3.4 - - - -
28x LYS* 1.3 80.1 - - - +
30x GLU* 1.3 57.7 + - - +
32x LEU* 3.9 5.7 - - - +
33x VAL* 2.9 32.6 + - - +
76x CYS* 6.3 2.9 - - + -
79x PRO* 5.4 15.0 - - + -
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Residues in contact with GLU 30 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26x THR* 5.3 6.1 - - - -
27x THR* 3.8 19.3 + - - +
28x LYS 3.2 1.0 - - - -
29x TRP* 1.3 78.3 - - - +
31x TRP* 1.3 59.6 + - - +
33x VAL* 3.9 3.4 - - - +
34x ASN* 3.0 27.4 + - - +
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Residues in contact with TRP 31 (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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20x GLY 5.9 2.0 - - - +
21x THR 5.9 2.9 - - - +
26x THR* 5.7 6.0 - - - -
27x THR 3.8 7.4 + - - +
28x LYS* 3.5 5.8 + - - +
30x GLU* 1.3 78.7 - - - +
32x LEU* 1.3 57.6 + - - +
34x ASN* 3.8 7.0 - - - +
35x GLN* 2.9 28.1 + - - +
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Residues in contact with LEU 32 (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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1295u TYR* 5.8 9.2 - - + -
28x LYS 3.0 19.8 + - - +
29x TRP* 3.9 6.7 - - - +
30x GLU 3.2 0.2 - - - -
31x TRP* 1.3 74.6 - - - +
33x VAL* 1.3 59.7 + - - +
35x GLN* 3.3 7.7 + - - +
36x HIS* 2.9 28.2 + - - +
76x CYS* 5.7 8.3 - - + -
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Residues in contact with VAL 33 (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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29x TRP 2.9 18.9 + - - +
30x GLU* 4.1 3.4 - - - +
32x LEU* 1.3 74.3 - - - +
34x ASN* 1.3 61.1 + - - +
36x HIS* 3.4 6.4 + - - +
37x ARG* 2.9 29.8 + - - +
75x PRO* 6.0 3.8 - - + +
76x CYS* 5.2 14.5 - - + +
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Residues in contact with ASN 34 (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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20x GLY* 4.0 31.6 - - - +
30x GLU 3.0 16.1 + - - +
31x TRP* 3.9 7.4 - - - +
33x VAL* 1.3 78.1 - - - +
35x GLN* 1.3 56.2 + - - +
37x ARG* 3.5 5.6 + - - +
38x ASP* 2.9 30.3 + - - +
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Residues in contact with GLN 35 (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 TRP 2.9 18.3 + - - +
32x LEU* 3.4 9.2 - - - +
34x ASN* 1.3 76.4 - - - +
36x HIS* 1.3 56.4 + - - +
38x ASP* 3.4 7.3 + - - +
39x SER* 2.9 28.6 + - - -
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Residues in contact with HIS 36 (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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32x LEU 2.9 16.5 + - - +
33x VAL* 3.9 6.1 - - - +
35x GLN* 1.3 73.9 - - - +
37x ARG* 1.3 61.1 + - - +
39x SER* 3.3 6.8 + - - -
40x TYR* 2.9 28.4 + - - +
75x PRO* 4.0 26.7 - - + -
76x CYS* 5.7 1.8 - - + +
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Residues in contact with ARG 37 (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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114v ARG* 5.3 5.9 - - + +
33x VAL 2.9 18.5 + - - +
34x ASN* 3.9 5.8 - - - +
36x HIS* 1.3 73.4 - - - +
38x ASP* 1.3 60.6 + - - +
40x TYR* 3.3 6.6 + - - +
41x CYS* 2.9 29.9 + - - +
72x MET* 5.2 18.8 - - + +
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Residues in contact with ASP 38 (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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1277u GLN* 5.9 4.5 - - + +
1281u ILE* 5.3 4.8 - - + +
114v ARG* 5.4 6.5 - - + +
34x ASN 2.9 18.8 + - - +
35x GLN* 3.6 7.2 - - - +
36x HIS 3.3 0.2 - - - -
37x ARG* 1.3 77.4 - - - +
39x SER* 1.3 56.9 + - - +
41x CYS* 3.4 5.8 + - - +
42x SER* 2.9 28.8 + - - -
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Residues in contact with SER 39 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281u ILE* 5.4 6.1 - - - -
1297u ARG* 5.6 10.3 - - - -
35x GLN 2.9 17.4 + - - -
36x HIS* 3.6 7.9 - - - -
37x ARG 3.3 0.2 - - - -
38x ASP* 1.3 76.6 - - - +
40x TYR* 1.3 56.4 + - - +
42x SER* 3.2 8.2 + - - -
43x TYR* 2.9 27.2 + - - +
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Residues in contact with TYR 40 (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 HIS 2.9 16.5 + - - +
37x ARG* 3.7 7.6 - - - +
38x ASP 3.3 0.2 - - - -
39x SER* 1.3 76.3 - - - +
41x CYS* 1.3 59.0 + - - +
43x TYR* 3.2 8.0 + - - +
44x MET* 2.9 29.6 + - - +
68x LEU* 4.1 25.9 - - + +
71x LYS 6.2 0.4 - - - -
72x MET* 5.2 10.1 - - + +
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Residues in contact with CYS 41 (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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112v CYS* 4.4 6.7 - - - +
113v ARG 4.3 18.7 - - - +
114v ARG* 4.4 17.7 - - + +
135v ILE* 5.7 7.4 - - + -
37x ARG 2.9 17.4 + - - +
38x ASP* 3.9 4.5 - - - +
39x SER 3.3 0.4 - - - -
40x TYR* 1.3 74.0 - - - +
42x SER* 1.3 59.5 + - - +
44x MET* 4.5 3.5 - - - +
45x GLY* 2.9 27.2 + - - -
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Residues in contact with SER 42 (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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1278u ASP* 5.6 5.6 - - - -
1281u ILE* 4.3 22.0 - - - -
112v CYS* 4.6 15.9 + - - +
38x ASP 2.9 18.3 + - - -
39x SER* 3.2 6.7 + - - -
41x CYS* 1.3 78.1 - - - +
43x TYR* 1.3 61.1 + - - +
45x GLY 4.6 0.2 - - - +
46x HIS* 3.4 24.3 + - - +
49x LEU* 4.5 2.5 - - - +
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Residues in contact with TYR 43 (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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1299u GLU* 6.4 1.6 - - + -
39x SER 2.9 13.9 + - - +
40x TYR* 3.2 12.3 + - - +
42x SER* 1.3 78.2 - - - +
44x MET* 1.3 56.9 + - - +
46x HIS 3.0 20.6 - - - +
49x LEU* 4.0 15.2 - - + +
50x LEU* 3.8 15.0 + - - +
68x LEU* 5.7 7.2 - - + -
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Residues in contact with MET 44 (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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40x TYR 2.9 15.2 + - - +
41x CYS* 4.5 3.6 - - - +
43x TYR* 1.3 75.0 - - - +
45x GLY* 1.3 65.0 + - - +
46x HIS 4.0 3.3 - - - +
50x LEU* 5.6 2.9 - - - +
65x ARG* 5.8 11.4 - - + +
68x LEU* 6.0 4.9 - - + -
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Residues in contact with GLY 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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61v VAL* 4.9 7.6 - - - +
63v ARG* 4.5 20.8 - - - +
112v CYS* 4.6 14.1 - - - -
119v GLN* 6.2 4.5 - - - -
41x CYS 2.9 19.3 + - - -
44x MET* 1.3 77.8 - - - +
46x HIS* 1.3 62.9 + - - +
47x PHE 3.6 1.7 + - - -
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Residues in contact with HIS 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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61v VAL* 5.3 7.4 - - + -
112v CYS* 5.0 2.4 - - - +
1098v GLY 6.0 0.2 - - - +
42x SER 3.4 18.4 + - - +
43x TYR 3.0 18.4 - - - +
44x MET 4.0 3.1 - - - +
45x GLY* 1.3 76.2 - - - +
47x PHE* 1.3 63.4 + - - +
48x ASP* 4.1 5.4 - - + +
49x LEU* 4.1 17.9 - - + +
50x LEU* 3.7 6.4 + - - +
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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
------------------------------------------------------------
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