Contacts of the helix formed by residues 24 - 38 (chain B) in PDB entry 3UVH
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 CYS 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS* 3.7 20.9 - - + -
21B ILE* 6.1 0.3 - - - +
22B GLY 3.1 8.0 + - - +
23B ASN* 1.3 75.8 + - - +
25B PRO* 1.3 71.8 - - - +
26B PHE* 3.5 20.4 - - - -
27B SER* 3.2 38.2 - - - +
28B GLN* 3.3 20.8 + - - +
64B LEU 4.8 3.6 - - - -
65B PRO* 4.2 8.7 - - - -
224B PRO* 4.8 4.2 - - - +
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Residues in contact with PRO 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN* 4.5 4.9 - - - +
24B CYS* 1.3 86.9 - - - +
26B PHE* 1.3 80.1 + - + +
28B GLN* 4.4 0.9 - - + +
29B ARG* 3.0 27.9 + - - +
111B PHE* 5.0 8.3 - - + -
179B ASN 5.4 1.1 - - - +
182B PRO* 3.8 26.7 - - + +
183B LYS* 4.0 22.4 - - + -
186B ILE* 3.8 26.9 - - + -
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU 4.0 25.4 - - - -
161A GLY 5.3 3.1 - - - -
24B CYS* 3.2 13.5 - - - -
25B PRO* 1.3 93.7 - - + +
27B SER* 1.3 64.6 + - - +
29B ARG* 3.4 13.9 + - - +
30B LEU* 3.3 27.4 + - - +
64B LEU 5.2 0.9 - - - -
65B PRO* 3.8 9.0 - - + -
77B THR* 3.3 27.3 + - + +
183B LYS* 4.6 17.5 - - - -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.1 3.6 - - - +
12B VAL* 3.6 24.4 - - - -
13B LYS 3.1 24.0 + - - -
21B ILE* 6.4 2.0 - - - -
24B CYS* 3.2 24.1 - - - +
26B PHE* 1.3 75.6 - - - +
28B GLN* 1.3 60.4 + - - +
30B LEU* 3.4 2.6 + - - +
31B PHE* 2.9 32.4 + - - +
65B PRO* 3.7 16.1 - - - +
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Residues in contact with GLN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 6.4 1.1 - - + -
24B CYS 3.3 13.7 + - - +
25B PRO* 3.9 4.3 - - - +
26B PHE 3.2 0.6 - - - -
27B SER* 1.3 81.2 - - - +
29B ARG* 1.3 57.2 + - - +
31B PHE* 3.2 7.5 + - - +
32B MET* 2.8 30.2 + - - +
182B PRO* 3.2 31.2 - - + +
185B HIS* 5.1 1.7 - - - -
219B PHE* 3.4 19.0 + - - -
222B THR* 3.1 42.5 + - - +
223B CYS* 3.3 26.3 - - - +
224B PRO* 3.8 14.3 - - + +
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO 3.0 18.7 + - - +
26B PHE* 3.5 12.2 - - - +
28B GLN* 1.3 75.4 - - - +
30B LEU* 1.3 60.3 + - + +
32B MET* 3.2 5.0 + - - +
33B VAL* 3.0 35.9 + - + +
77B THR* 3.5 29.1 - - + +
78B ASN* 2.8 43.0 + - - +
81B MET* 3.2 31.6 - - - +
175B LEU 5.2 0.2 + - - -
178B CYS* 3.4 32.2 - - + +
179B ASN* 3.8 41.4 + - - +
182B PRO* 4.1 1.2 - - - +
183B LYS* 5.4 1.6 - - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.9 22.2 - - + -
26B PHE 3.3 10.8 + - - +
27B SER 4.0 1.8 - - - +
29B ARG* 1.3 78.4 - - + +
31B PHE* 1.3 66.1 + - - +
33B VAL* 3.8 5.5 - - + +
34B LEU* 3.0 30.1 + - + +
65B PRO* 3.7 32.3 - - + -
77B THR* 3.8 32.1 - - + +
80B ILE* 3.9 38.8 - - + -
81B MET* 4.3 13.0 - - + +
84B LEU* 4.8 6.7 - - + +
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.5 13.6 - - + +
12B VAL* 5.1 4.3 - - + -
21B ILE* 5.2 11.7 - - + -
27B SER 2.9 20.0 + - - +
28B GLN* 3.4 7.2 - - - +
30B LEU* 1.3 78.5 - - - +
32B MET* 1.3 62.4 + - - +
34B LEU* 3.5 2.1 + - - +
35B TRP* 3.1 38.2 + + - +
41B PHE* 3.8 23.8 - + - -
43B VAL* 4.0 28.0 - - + -
221B SER 5.0 4.3 - - - -
222B THR* 3.6 36.8 - - + -
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Residues in contact with MET 32 (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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28B GLN* 2.8 13.8 + - - +
29B ARG 3.2 8.3 + - - +
31B PHE* 1.3 75.0 - - - +
33B VAL* 1.3 60.0 + - - +
35B TRP* 3.3 6.8 + - - +
36B LEU* 3.0 34.8 + - + +
173B LEU* 4.8 14.4 - - + -
178B CYS* 3.6 33.4 - - - +
181B LEU* 4.0 21.1 - - + -
182B PRO* 4.1 21.1 - - - -
218B GLU* 3.4 23.7 - - + +
219B PHE* 3.9 31.4 - - + +
222B THR* 3.6 8.3 - - - +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ARG* 3.0 23.7 + - + +
30B LEU* 3.8 8.7 - - + +
31B PHE 3.3 0.2 - - - -
32B MET* 1.3 71.8 - - - +
34B LEU* 1.3 68.3 + - - +
36B LEU* 3.0 16.3 + - - +
37B LYS* 3.0 26.7 + - + +
81B MET* 4.4 14.4 - - + -
84B LEU* 3.9 29.4 - - + -
96B LEU* 4.6 1.3 - - + -
175B LEU* 3.7 33.4 - - + -
178B CYS* 3.7 20.2 - - + -
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Residues in contact with LEU 34 (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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8B VAL* 4.0 24.2 - - + -
10B LEU* 3.8 25.1 - - + -
30B LEU 3.0 22.0 + - - +
31B PHE 3.8 0.2 - - - +
33B VAL* 1.3 78.1 - - - +
35B TRP* 1.3 61.3 + - - +
37B LYS* 3.2 12.9 + - - +
38B GLY 3.5 8.3 + - - -
39B VAL* 3.7 20.7 + - + +
41B PHE* 3.4 43.7 - - + -
67B LEU* 4.3 6.3 - - + -
84B LEU* 3.4 31.6 - - + -
88B LEU* 4.4 4.7 - - + -
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Residues in contact with TRP 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 PHE* 3.1 37.2 + + - +
32B MET* 3.4 9.9 - - - +
33B VAL 3.2 0.2 - - - -
34B LEU* 1.3 75.8 - - - +
36B LEU* 1.3 62.5 + - - +
38B GLY* 3.3 13.2 + - - -
41B PHE* 3.7 12.0 - + + -
217B GLU* 3.6 35.0 - - + +
218B GLU* 3.4 34.1 + - + +
221B SER* 3.7 34.5 - - - -
222B THR* 3.8 16.4 - - + -
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Residues in contact with LEU 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 MET* 3.0 23.0 + - + +
33B VAL 3.0 0.4 + - - +
35B TRP* 1.3 75.6 - - - +
37B LYS* 1.3 64.6 + - - +
38B GLY* 3.5 0.5 + - - -
94B PRO* 3.6 16.1 - - - +
96B LEU* 3.4 28.7 - - + +
173B LEU* 3.7 38.1 - - + +
174B THR 5.4 0.2 - - - -
178B CYS* 3.6 23.3 - - - -
216B ARG* 3.8 26.0 - - - +
218B GLU* 4.0 17.3 - - + +
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Residues in contact with LYS 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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33B VAL* 3.0 24.1 + - + +
34B LEU* 3.2 9.6 + - - +
36B LEU* 1.3 76.7 - - - +
38B GLY* 1.3 58.8 + - - +
39B VAL 3.3 1.3 - - - +
84B LEU* 3.9 12.1 - - + +
85B GLU* 2.7 35.1 + - - +
88B LEU* 2.8 56.3 + - + +
89B CYS* 4.8 0.6 - - - +
92B ARG* 5.3 0.3 + - - -
93B TYR* 3.2 21.2 - - + -
94B PRO* 2.6 44.9 + - - +
95B LYS* 3.8 1.8 - - - +
96B LEU* 3.7 14.1 - - + +
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Residues in contact with GLY 38 (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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34B LEU 3.5 2.0 + - - -
35B TRP 3.3 11.4 + - - -
36B LEU 3.2 4.0 - - - -
37B LYS* 1.3 77.6 - - - +
39B VAL* 1.3 66.7 + - - +
40B THR* 5.0 1.4 + - - -
92B ARG* 4.6 10.0 + - - -
93B TYR* 4.2 6.7 - - - -
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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