Contacts of the helix formed by residues 38 - 51 (chain A) in PDB entry 4KPF
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 LYS 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ARG 3.3 13.2 - - - +
29A ALA* 3.3 24.0 + - - +
30A LEU 4.1 12.1 - - - +
31A PRO* 4.6 1.8 - - + -
36A GLY 5.3 0.2 - - - +
37A LEU* 1.3 73.9 - - - +
39A PRO* 1.3 80.5 - - + +
40A VAL* 4.5 7.4 - - + +
41A GLN* 2.8 42.8 + - + +
42A ARG* 3.1 9.4 + - - -
167A SER* 4.3 12.8 - - - +
168A THR 2.8 35.4 + - - +
169A GLY 3.4 4.6 - - - +
170A ILE 5.3 0.4 - - - +
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Residues in contact with PRO 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN 4.7 2.0 - - - +
27A ASP* 3.0 44.9 - - - +
28A ARG* 3.6 14.1 - - - +
30A LEU 4.5 4.7 - - - +
37A LEU 4.8 0.2 - - - +
38A LYS* 1.3 88.8 - - + +
40A VAL* 1.3 57.3 + - - +
42A ARG* 3.3 21.7 + - - +
43A ARG* 2.9 54.7 + - - +
74A HIS* 5.5 1.1 - - + -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG 5.8 1.6 - - - +
38A LYS* 3.0 9.7 + - + +
39A PRO* 1.3 78.5 - - - +
41A GLN* 1.3 81.3 + - + +
43A ARG* 3.2 4.2 + - - +
44A ILE* 2.8 39.1 + - + +
74A HIS* 3.2 47.0 - - + +
80A SER* 5.3 1.8 - - - +
81A ILE* 4.5 19.7 - - + +
84A ALA* 4.1 14.4 - - + -
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 4.2 3.3 - - - +
37A LEU* 3.6 22.0 - - + +
38A LYS* 2.8 53.8 + - - +
40A VAL* 1.3 89.6 - - + +
42A ARG* 1.3 61.9 + - - +
44A ILE* 3.1 4.3 + - - +
45A LEU* 2.9 27.3 + - - +
84A ALA* 5.2 2.5 - - + -
87A ARG* 4.9 14.5 - - - +
88A MET* 3.1 40.9 - - + +
94A ASN* 5.9 2.2 - - - +
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 3.5 15.6 - - - +
35A ASP* 2.8 32.4 + - - -
37A LEU* 2.9 40.3 + - + +
38A LYS 3.1 6.6 + - - +
39A PRO* 3.6 27.0 - - - +
41A GLN* 1.3 75.0 - - - +
43A ARG* 1.3 58.5 + - + +
45A LEU* 3.2 3.3 + - - +
46A TYR* 2.8 31.8 + - - +
152A PRO* 3.5 26.9 + - + +
153A THR* 3.3 23.5 + - - +
154A VAL* 3.5 7.8 - - - +
155A LEU* 3.7 21.9 - - + +
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 5.1 7.1 + - - -
27A ASP 5.6 1.2 + - - -
39A PRO* 2.9 40.9 + - - +
40A VAL 3.5 4.5 - - - +
42A ARG* 1.3 72.5 - - - +
44A ILE* 1.3 64.7 + - - +
46A TYR* 4.0 4.4 - - - +
47A SER* 2.9 28.7 + - - -
69A ILE* 4.7 4.5 - - + -
73A PHE* 3.3 41.2 + - + -
74A HIS* 3.1 43.5 + - + +
75A PRO* 4.2 6.9 - - - +
145A PHE* 5.8 2.0 - - - +
151A GLU* 2.9 39.0 + - - +
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 2.8 18.0 + - + +
41A GLN 3.3 7.0 - - - +
43A ARG* 1.3 77.1 - - - +
45A LEU* 1.3 67.7 + - + +
47A SER* 3.9 0.7 - - - -
48A MET* 3.1 41.0 + - - +
69A ILE* 3.6 27.1 - - + +
81A ILE* 3.5 31.4 - - + +
84A ALA* 3.7 7.2 - - + -
85A MET* 3.5 18.8 - - + +
88A MET* 3.1 33.4 - - + -
99A VAL* 4.8 2.9 - - + -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.1 15.5 - - + -
41A GLN 2.9 19.3 + - - +
42A ARG 3.9 4.3 - - - +
44A ILE* 1.3 72.4 - - + +
46A TYR* 1.3 63.9 + - - +
49A ASN* 3.0 25.8 + - - +
88A MET* 4.3 13.7 - - - -
98A LEU* 4.1 31.9 - - + +
99A VAL* 4.3 4.9 - - + -
123A LEU* 3.4 30.2 - - + +
127A ALA* 4.7 5.6 - - + +
130A LEU* 4.0 31.4 - - + -
131A LEU* 3.9 12.5 - - + +
155A LEU* 4.1 5.4 - - + -
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Residues in contact with TYR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG 2.8 20.8 + - - +
43A ARG* 4.0 4.0 - - - +
45A LEU* 1.3 73.3 - - - +
47A SER* 1.3 59.1 + - - +
49A ASN* 3.4 3.1 + - + +
50A LYS* 2.9 48.3 + - + +
73A PHE* 3.4 42.2 - + - -
131A LEU* 4.2 12.7 - - + +
134A ILE* 3.8 21.3 - - + -
141A PHE* 3.9 23.6 - + - -
149A GLU* 4.5 2.6 + - - +
150A LYS 4.0 8.6 + - - -
151A GLU* 4.7 0.4 - - + -
152A PRO* 3.5 39.5 - - + -
155A LEU* 4.8 1.3 - - + -
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG 2.9 18.6 + - - -
44A ILE 3.9 0.2 - - - -
46A TYR* 1.3 74.9 - - - +
48A MET* 1.3 66.9 - - - +
50A LYS* 2.9 16.2 + - - +
51A ASP* 3.0 23.9 + - - +
65A SER* 4.5 0.9 + - - -
68A ASN* 4.0 3.8 - - - +
69A ILE* 3.5 34.8 + - - +
72A ASN* 4.9 1.0 + - - -
73A PHE* 3.8 24.9 - - - -
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Residues in contact with MET 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 3.1 32.7 + - + +
47A SER* 1.3 76.2 + - - +
49A ASN* 1.3 61.4 + - - +
51A ASP* 3.2 7.7 + - - -
52A SER 3.1 3.6 + - - -
53A ASN* 3.0 42.1 + - + +
65A SER* 4.3 19.7 - - - +
69A ILE* 5.0 4.0 - - + -
85A MET* 4.3 18.4 - - - +
99A VAL* 4.6 7.9 - - + -
121A ALA* 4.4 2.9 - - + -
122A ARG* 3.3 20.2 - - - +
123A LEU* 3.3 49.1 - - + +
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Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU 3.0 19.2 + - - +
46A TYR* 3.6 6.8 - - + +
48A MET* 1.3 73.8 - - - +
50A LYS* 1.3 67.2 + - - +
51A ASP 2.9 1.8 - - - -
52A SER* 3.0 15.1 + - - +
54A THR* 3.8 21.4 - - - +
123A LEU* 3.7 6.2 - - + +
128A GLY* 5.4 3.8 - - - -
131A LEU* 3.4 37.1 - - + +
134A ILE* 4.5 12.5 - - - +
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR* 2.9 38.6 + - + +
47A SER* 2.9 6.9 + - - +
49A ASN* 1.3 77.5 + - - +
51A ASP* 1.3 65.7 + - - +
52A SER* 3.5 4.5 + - - -
72A ASN* 6.1 2.5 - - - +
73A PHE* 4.6 6.3 - - + -
149A GLU* 3.5 25.4 - - - +
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 3.0 18.5 + - - +
48A MET* 3.5 11.5 - - - +
49A ASN 2.9 0.4 - - - -
50A LYS* 1.3 86.8 - - - +
52A SER* 1.3 58.9 + - - +
53A ASN* 3.1 1.3 - - + +
60A ARG* 2.6 43.5 + - - +
64A LYS* 6.5 1.1 - - - -
65A SER* 5.4 4.3 - - - -
68A ASN* 3.9 28.6 + - - +
72A ASN* 5.6 1.0 + - - -
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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