Contacts of the helix formed by residues 30 - 46 (chain B) in PDB entry 1I7K
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 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE 4.8 4.7 - - - +
145A ASP* 3.9 18.4 - - - +
147A PRO* 3.9 29.8 - - + -
150A THR* 4.4 15.4 - - + -
153A ALA* 6.1 0.7 - - + -
31B VAL* 1.3 65.4 + - - +
32B GLY 3.4 2.5 - - - +
33B LYS* 3.7 23.8 - - + +
34B ARG* 3.2 20.0 + - - +
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A THR* 4.4 11.2 - - + -
30B PRO* 1.3 69.8 - - - +
32B GLY* 1.3 61.0 + - - +
34B ARG* 3.2 7.3 + - - +
35B LEU* 2.9 40.6 + - + +
60B PHE* 3.7 29.2 - - + -
85B PHE* 5.4 0.7 - - + -
86B PRO 4.8 3.8 - - - +
87B SER* 3.7 20.6 - - - +
89B TYR* 3.7 37.7 - - + +
90B PRO* 6.1 0.2 - - - -
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO* 3.4 0.8 - - - +
31B VAL* 1.3 80.0 - - - +
33B LYS* 1.3 61.9 + - - +
35B LEU* 3.3 3.0 + - - +
36B GLN* 3.0 32.3 + - - +
59B LEU* 3.7 22.2 - - - +
60B PHE* 4.9 6.9 - - - -
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP 5.9 1.1 - - - +
30B PRO* 3.4 29.2 + - + +
31B VAL 3.2 0.6 - - - -
32B GLY* 1.3 76.7 - - - +
34B ARG* 1.3 63.8 + - - +
36B GLN* 3.3 35.5 - - - +
37B GLN* 3.1 25.2 + - - +
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PRO 4.9 2.2 + - - -
148A LEU* 4.6 7.9 - - - +
30B PRO 3.2 12.8 + - - +
31B VAL* 3.5 9.9 - - - +
33B LYS* 1.3 80.8 - - - +
35B LEU* 1.3 62.5 + - - +
37B GLN* 3.1 29.3 + - - +
38B GLU* 2.6 55.3 + - - +
89B TYR* 3.9 15.6 + - + -
90B PRO* 3.5 33.4 - - + +
124B ALA 3.1 23.8 + - - -
125B LEU 4.5 1.2 - - - -
126B TYR 2.8 29.7 + - - -
127B ASP* 4.4 2.0 - - - +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 2.9 37.1 + - + +
32B GLY 3.3 3.8 + - - +
34B ARG* 1.3 77.7 - - - +
36B GLN* 1.3 61.6 + - - +
38B GLU* 3.2 9.5 + - - +
39B LEU* 3.0 19.6 + - - +
59B LEU* 3.4 39.3 - - + +
60B PHE* 4.1 13.9 - - + -
62B TRP* 3.7 20.8 - - + -
85B PHE* 3.9 44.6 - - + -
89B TYR* 4.0 13.0 - - + -
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Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLY 3.0 20.5 + - - +
33B LYS* 3.3 28.1 - - - +
34B ARG 3.3 0.2 - - - -
35B LEU* 1.3 75.9 - - - +
37B GLN* 1.3 64.3 + - - +
39B LEU* 3.2 9.0 + - - +
40B MET* 3.0 29.5 + - + +
59B LEU* 4.4 20.6 - - + +
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Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER* 5.4 5.3 + - - -
33B LYS* 3.1 23.9 + - - +
34B ARG* 3.4 36.4 + - - +
36B GLN* 1.3 77.6 - - - +
38B GLU* 1.3 65.5 + - + +
40B MET* 3.2 9.9 + - - +
41B THR* 2.8 37.9 + - + +
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 2.6 44.8 + - - +
35B LEU* 3.2 12.3 + - - +
37B GLN* 1.3 78.8 - - + +
39B LEU* 1.3 64.9 + - - +
41B THR* 3.4 9.4 + - + -
42B LEU* 3.0 24.1 + - - +
62B TRP* 4.4 9.2 - - + -
89B TYR* 2.5 33.0 + - - -
127B ASP* 3.5 21.1 - - + +
128B VAL* 2.7 38.9 + - + +
129B ARG* 5.8 1.0 + - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU 3.0 9.3 + - - +
36B GLN* 3.2 10.5 + - - +
38B GLU* 1.3 77.1 - - - +
40B MET* 1.3 63.5 + - + +
42B LEU* 3.2 8.2 + - + +
43B MET* 3.0 39.1 + - + +
52B ALA 3.5 24.5 - - - +
53B PHE* 3.8 19.7 - - + -
54B PRO* 3.9 23.6 - - + -
59B LEU* 6.3 0.4 - - + -
62B TRP* 3.7 24.8 - - + -
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Residues in contact with MET 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLN* 3.0 23.2 + - + +
37B GLN* 3.2 11.4 + - - +
39B LEU* 1.3 78.3 - - + +
41B THR* 1.3 64.3 + - + +
43B MET* 3.4 14.1 + - - +
44B MET* 3.0 25.8 + - - +
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLN* 2.8 30.9 + - + +
38B GLU* 4.0 6.8 + - - +
39B LEU 3.4 0.2 - - - -
40B MET* 1.3 76.8 - - + +
42B LEU* 1.3 65.2 + - - +
44B MET* 3.8 5.6 - - - +
45B SER* 2.8 35.5 + - - -
127B ASP* 3.7 19.4 + - - +
129B ARG* 4.6 5.9 - - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLU 3.0 17.4 + - - +
39B LEU* 3.2 7.4 + - + +
41B THR* 1.3 81.6 + - - +
43B MET* 1.3 62.9 + - + +
44B MET 3.4 0.2 + - - -
45B SER* 3.4 10.6 + - - -
46B GLY* 3.6 9.0 + - - -
47B ASP* 5.0 2.1 + - - +
50B ILE* 3.9 33.4 - - + +
51B SER* 5.3 1.8 - - - -
52B ALA* 3.7 45.1 - - + +
62B TRP* 4.3 7.4 - - + -
128B VAL* 4.1 13.5 - - + -
129B ARG* 4.0 24.9 - - + +
132B LEU* 4.5 4.0 - - + -
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Residues in contact with MET 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.0 35.1 + - + +
40B MET* 3.8 17.7 - - - +
42B LEU* 1.3 78.9 - - - +
44B MET* 1.3 60.4 + - - +
46B GLY* 3.7 8.9 + - - -
53B PHE* 4.4 22.9 - - + -
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Residues in contact with MET 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET 3.0 18.7 + - - +
41B THR* 3.8 6.7 - - - +
43B MET* 1.3 76.8 - - - +
45B SER* 1.3 66.3 + - - +
46B GLY* 3.6 0.6 + - - -
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B THR* 2.8 24.9 + - - -
42B LEU 3.8 4.0 - - - -
43B MET 3.3 0.4 - - - -
44B MET* 1.3 82.1 - - - +
46B GLY* 1.3 64.3 + - - +
47B ASP* 3.3 23.9 + - - +
129B ARG* 3.5 22.8 + - - -
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU 3.6 8.7 + - - -
43B MET 3.7 7.2 + - - -
44B MET 3.4 3.0 - - - -
45B SER* 1.3 79.3 - - - +
47B ASP* 1.3 67.8 + - - +
48B LYS* 3.7 8.0 + - - +
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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