Contacts of the helix formed by residues 31 - 45 (chain A) in PDB entry 4KMD
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 PRO 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A SER* 4.7 8.5 - - - +
29A LEU 3.7 7.9 - - - +
30A PHE* 1.3 90.9 - - + +
32A PRO* 1.3 66.1 - - + +
33A GLY 3.3 0.2 - - - -
34A LEU* 3.1 27.3 + - + +
35A HIS* 2.9 26.7 + - - +
98A LEU 3.2 17.7 - - - +
99A TYR* 3.5 34.3 - - + -
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Residues in contact with PRO 32 (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 SER* 4.7 9.2 - - - +
30A PHE 3.5 7.6 - - - +
31A PRO* 1.3 83.2 - - + +
33A GLY* 1.3 56.8 + - - +
35A HIS* 3.9 8.0 + - + +
36A ALA* 3.1 27.7 + - - +
98A LEU 4.1 0.9 - - - +
99A TYR 4.3 5.8 - - - +
191A PRO* 3.7 25.7 - - + +
192A PHE* 3.7 28.9 - - + -
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Residues in contact with GLY 33 (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 PRO* 1.3 76.3 - - - +
34A LEU* 1.3 66.1 + - - +
36A ALA* 3.6 2.6 + - - +
37A ILE* 3.4 27.3 + - - +
96A SER* 5.7 0.4 - - - -
97A ASP 3.6 15.3 - - - -
98A LEU* 3.0 20.2 + - - -
190A THR* 4.3 13.7 - - - +
192A PHE* 3.6 7.6 - - - -
195A VAL* 5.9 0.2 - - - +
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Residues in contact with LEU 34 (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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30A PHE* 4.5 4.3 - - + -
31A PRO* 3.1 39.6 + - + +
33A GLY* 1.3 77.1 - - - +
35A HIS* 1.3 61.3 + - - +
37A ILE* 3.3 4.0 + - - +
38A TYR* 3.1 63.8 + - + +
70A TYR* 4.2 23.3 - - + +
93A PHE* 3.6 35.9 - - + -
98A LEU* 3.6 19.0 + - + +
99A TYR* 5.6 0.4 - - + -
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Residues in contact with HIS 35 (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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30A PHE* 3.7 36.3 - + + +
31A PRO 2.9 15.5 + - - +
32A PRO* 3.9 8.4 + - + +
34A LEU* 1.3 75.5 - - - +
36A ALA* 1.3 65.4 + - - +
38A TYR* 3.4 7.0 + - + +
39A GLY* 3.1 19.7 + - - -
42A ARG* 3.7 22.5 + - - -
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Residues in contact with ALA 36 (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 PRO 3.1 18.2 + - - +
33A GLY 3.9 0.9 - - - +
34A LEU 3.3 0.2 - - - -
35A HIS* 1.3 80.0 + - - +
37A ILE* 1.3 61.5 + - - +
39A GLY* 3.3 10.8 + - - -
40A GLU 3.6 6.1 + - - -
188A VAL* 3.4 18.9 - - + +
189A GLN 4.0 6.3 - - - +
190A THR* 3.5 32.1 - - + -
191A PRO* 4.9 1.6 - - + -
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Residues in contact with ILE 37 (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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33A GLY 3.4 14.8 + - - +
34A LEU 3.3 3.4 + - - +
36A ALA* 1.3 73.7 - - + +
38A TYR* 1.3 66.6 + - - +
40A GLU* 2.9 14.6 + - - +
41A CYS* 3.0 17.8 + - - -
91A ILE* 4.6 1.3 - - + -
93A PHE* 3.4 41.5 - - + -
96A SER* 3.7 23.1 - - - +
98A LEU* 4.4 2.2 - - + -
119A GLU* 4.0 13.2 - - + +
185A MET* 4.4 0.9 - - + -
188A VAL* 4.5 9.6 - - + -
190A THR* 5.1 0.4 - - + -
195A VAL* 4.3 14.6 - - + -
197A PHE* 3.7 31.0 - - + -
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Residues in contact with TYR 38 (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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30A PHE* 3.7 32.3 - + - -
34A LEU* 3.1 41.3 + - + +
35A HIS* 3.5 11.2 - - + +
37A ILE* 1.3 74.5 - - - +
39A GLY* 1.3 57.9 + - - +
41A CYS* 3.2 10.1 + - + +
42A ARG* 2.8 37.8 + - - +
53A GLN* 2.9 30.8 + - - -
70A TYR* 4.8 2.3 - - - -
72A SER* 4.7 2.0 - - - -
74A TYR* 5.7 1.3 - - - -
93A PHE* 3.5 34.8 - + - -
505A GOL 3.6 33.8 - - - +
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Residues in contact with GLY 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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35A HIS* 3.1 12.9 + - - -
36A ALA* 3.3 6.7 + - - -
37A ILE 3.1 0.8 - - - -
38A TYR* 1.3 77.0 - - - +
40A GLU* 1.3 55.4 + - - +
42A ARG* 3.5 24.8 + - - +
43A ARG* 3.1 26.2 + - - +
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ALA 3.6 4.0 + - - -
37A ILE 2.9 9.4 + - - +
39A GLY* 1.3 73.6 - - - +
41A CYS* 1.3 64.8 + - - +
43A ARG* 2.7 46.6 + - - +
44A LEU* 3.2 22.4 + - - +
185A MET* 3.6 28.4 - - + -
186A GLN* 2.8 40.0 + - - +
188A VAL* 3.6 20.2 - - + +
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Residues in contact with CYS 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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37A ILE* 3.0 24.9 + - - -
38A TYR* 3.5 11.7 - - - +
40A GLU* 1.3 75.7 - - - +
42A ARG* 1.3 50.8 + - - +
44A LEU* 3.2 1.3 + - - -
45A TYR* 2.8 44.7 + - - +
72A SER* 5.7 0.4 - - - -
74A TYR* 3.4 27.8 - - + +
91A ILE* 3.6 30.3 - - - -
93A PHE* 4.5 10.5 - - - -
185A MET* 4.2 11.9 - - - -
505A GOL 4.4 1.8 - - - -
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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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35A HIS* 3.7 28.7 + - - -
38A TYR* 2.8 15.0 + - - +
39A GLY* 3.7 28.2 + - - +
40A GLU 3.3 0.2 - - - -
41A CYS* 1.3 70.7 - - - +
43A ARG* 1.3 65.7 + - - +
45A TYR 4.4 6.5 - - - +
46A PRO* 3.0 31.3 - - + +
49A PRO* 5.9 1.8 - - + -
505A GOL 3.1 44.9 + - - +
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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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39A GLY 3.1 14.4 + - - +
40A GLU* 2.7 45.8 + - - +
42A ARG* 1.3 79.2 - - - +
44A LEU* 1.3 77.1 + - - +
46A PRO* 3.7 9.6 - - - +
184A GLN 3.8 9.3 + - - -
186A GLN* 3.5 29.9 - - - +
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Residues in contact with LEU 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 GLU* 3.2 10.1 + - - +
41A CYS 3.9 5.8 - - - +
43A ARG* 1.3 107.3 - - - +
45A TYR* 1.3 85.9 + - + +
46A PRO* 3.4 7.2 - - - +
47A ASP* 5.3 0.2 - - - +
89A HIS* 5.2 2.0 - - + -
184A GLN* 4.0 43.1 - - + +
185A MET* 3.4 40.4 - - + -
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Residues in contact with TYR 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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41A CYS* 2.8 19.8 + - - +
42A ARG* 3.4 7.9 - - - +
44A LEU* 1.3 100.9 - - + +
46A PRO* 1.4 64.6 - - - +
47A ASP* 3.1 8.1 - - - -
48A GLN* 3.0 38.6 + - + +
49A PRO* 5.1 0.2 - - - +
74A TYR* 3.6 49.1 - + + -
75A ARG 3.5 15.5 - - - -
76A ASN* 2.9 29.8 + - - -
89A HIS* 2.6 41.1 + + - +
91A ILE* 4.8 2.9 - - + -
123A ARG* 4.1 0.5 + - - -
505A GOL 4.8 0.7 + - - -
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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