Contacts of the helix formed by residues 30 - 41 (chain T) in PDB entry 6L49
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 30 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I A 3.4 40.7 + - - -
158I C 3.8 16.2 - - - +
63S ARG* 5.0 10.0 - - - +
27T GLN 4.5 4.9 - - - +
28T GLY* 3.1 16.5 + - - +
29T ILE* 1.3 77.4 - - - +
31T LYS* 1.3 64.1 + - - +
32T PRO* 3.9 0.6 - - - +
33T ALA* 3.2 30.9 + - - +
34T ILE* 3.2 14.4 + - - +
55T ARG* 3.5 2.7 - - - +
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Residues in contact with LYS 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158I C 4.1 14.8 + - - +
159I G 5.7 5.5 + - - -
-161J T 5.0 6.7 + - - -
30T THR* 1.3 74.7 - - - +
32T PRO* 1.3 65.1 - - + +
34T ILE* 3.3 6.0 + - - -
35T ARG* 2.9 52.8 + - - +
51T TYR* 3.6 39.0 - - + -
55T ARG* 3.4 15.4 - - - +
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Residues in contact with PRO 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I A 3.3 51.6 - - + +
158I C 3.5 17.7 - - - +
30T THR* 3.9 0.2 - - - +
31T LYS* 1.3 89.7 - - + +
33T ALA* 1.3 59.7 + - - +
35T ARG* 3.5 19.8 - - + +
36T ARG* 2.8 34.6 + - - +
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Residues in contact with ALA 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61S LEU* 3.8 12.3 - - - +
62S ILE* 4.5 8.3 - - + -
63S ARG* 5.2 4.5 - - + +
29T ILE* 4.8 7.2 - - + -
30T THR* 3.2 30.1 + - - +
31T LYS 3.2 1.2 - - - -
32T PRO* 1.3 74.8 - - - +
34T ILE* 1.3 58.5 + - - +
36T ARG* 3.2 28.8 + - - +
37T LEU* 2.9 31.8 + - - +
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Residues in contact with ILE 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100S LEU* 5.9 0.9 - - + -
104S PHE* 3.5 30.3 - - + -
29T ILE* 4.0 13.5 - - + +
30T THR 3.2 17.4 + - - +
31T LYS* 3.3 0.9 + - - +
33T ALA* 1.3 73.1 - - - +
35T ARG* 1.3 60.3 + - - +
37T LEU* 3.3 12.1 + - + -
38T ALA* 2.9 24.3 + - - +
51T TYR* 3.6 35.4 - - + +
54T THR* 3.7 20.0 - - + +
55T ARG* 3.5 39.9 - - + +
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Residues in contact with ARG 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-163J C 5.8 0.6 - - - +
-162J G 3.2 27.5 + - - +
-161J T 3.8 29.5 + - - +
50S GLU* 4.0 17.2 + - - +
54S TYR* 6.3 0.4 - - + -
31T LYS* 2.9 37.3 + - - +
32T PRO* 3.5 19.7 - - + +
33T ALA 3.2 0.2 - - - -
34T ILE* 1.3 77.6 - - - +
36T ARG* 1.3 56.4 + - + +
38T ALA* 3.1 2.9 + - - +
39T ARG* 2.9 64.3 + - + +
46T ILE* 3.7 18.9 + - + +
51T TYR* 3.1 26.7 + - + -
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Residues in contact with ARG 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I A 4.0 8.8 + - - -
157I A 2.7 42.0 + - - -
54S TYR* 3.6 53.6 + - + +
59S GLU* 5.4 3.1 + - - -
61S LEU* 2.8 59.6 + - + +
63S ARG* 4.6 10.3 - - - +
32T PRO* 2.8 18.3 + - + +
33T ALA* 3.2 21.8 + - - +
35T ARG* 1.3 74.9 - - + +
37T LEU* 1.3 58.2 + - - +
39T ARG* 3.3 1.6 + - - +
40T ARG* 2.9 24.3 + - - +
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Residues in contact with LEU 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61S LEU* 3.8 15.3 - - + -
62S ILE* 3.9 17.7 - - + -
97S GLU* 3.7 45.1 - - + +
100S LEU* 3.8 29.8 - - + -
101S VAL* 3.7 17.3 - - + +
104S PHE* 3.5 19.0 - - + +
29T ILE* 5.5 0.7 - - + -
33T ALA 2.9 19.2 + - - +
34T ILE* 3.5 21.1 - - + +
36T ARG* 1.3 76.3 - - - +
38T ALA* 1.3 56.8 + - - +
40T ARG 3.6 0.2 + - - -
41T GLY* 3.0 20.6 + - - -
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Residues in contact with ALA 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S PHE* 3.6 32.5 - - + -
34T ILE 2.9 13.7 + - - +
35T ARG 3.1 7.8 + - - +
37T LEU* 1.3 75.5 - - - +
39T ARG* 1.3 60.9 + - - +
41T GLY 3.1 2.4 + - - -
42T GLY 3.0 10.6 + - - -
43T VAL* 2.9 32.3 + - + +
46T ILE* 3.7 21.8 - - + -
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Residues in contact with ARG 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-162J G 4.1 4.2 + - - -
-161J T 4.6 2.6 + - - -
47S ALA* 3.4 35.8 + - - +
50S GLU* 3.2 47.3 + - + +
51S ILE* 3.4 20.8 - - - +
54S TYR* 3.8 9.6 - - + -
55S GLN* 3.3 15.1 + - - -
35T ARG* 2.9 48.9 + - + +
36T ARG 3.3 4.7 + - - +
38T ALA* 1.3 76.5 - - - +
40T ARG* 1.3 60.4 + - - +
42T GLY 3.3 2.8 + - - -
43T VAL 2.4 33.1 + - - -
44T LYS 2.7 26.1 + - - -
46T ILE* 3.4 20.4 - - - +
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Residues in contact with ARG 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54S TYR* 2.7 19.9 + - - +
55S GLN* 3.2 26.5 + - + +
57S SER* 2.7 40.3 + - - -
58S THR* 4.0 7.6 + - - +
59S GLU 3.2 22.2 + - - -
61S LEU* 3.5 18.7 - - + +
97S GLU* 3.6 22.4 + - - +
101S VAL* 3.7 29.8 - - + +
105S GLU* 4.3 2.8 - - - +
36T ARG 2.9 16.7 + - - +
37T LEU 3.9 0.2 - - - +
39T ARG* 1.3 75.7 - - - +
41T GLY* 1.3 57.2 + - - +
42T GLY 3.2 0.4 - - - -
106Y GLY* 5.0 9.7 - - - -
107Y VAL* 3.8 31.3 - - + +
108Y LEU 4.8 0.5 - - - +
110Y ASN* 5.6 0.2 - - - +
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Residues in contact with GLY 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S GLN* 4.3 0.7 - - - -
101S VAL* 3.7 21.3 - - - +
104S PHE* 3.8 6.9 - - - +
105S GLU* 3.3 32.1 + - - +
108S ASN* 4.6 0.9 - - - +
37T LEU 3.0 16.7 + - - -
38T ALA 3.1 6.4 + - - -
40T ARG* 1.3 76.6 - - - +
42T GLY* 1.3 61.1 + - - +
43T VAL* 4.4 1.6 - - - -
110Y ASN* 4.7 2.9 + - - -
112Y GLN* 5.2 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