Contacts of the strand formed by residues 38 - 46 (chain Q) in PDB entry 3QUM
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 ARG 38 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 6.5 0.2 - - - -
28C TYR* 4.9 7.9 - - - +
92C HIS* 5.9 2.4 + - - -
93C GLU* 5.7 2.6 + - - -
34Q ALA* 3.2 5.0 - - - +
35Q SER 2.9 32.0 + - - +
36Q ARG* 5.4 4.2 + - - +
37Q GLY* 1.3 89.8 + - - +
39Q ALA* 1.3 69.7 + - - +
150Q LEU* 6.0 6.5 - - - -
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Residues in contact with ALA 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR* 4.0 23.2 + - + +
32Q LEU* 3.3 28.3 - - + -
33Q VAL 3.9 0.7 - - - -
34Q ALA* 3.7 11.2 - - - +
38Q ARG* 1.3 84.6 - - - +
41Q VAL* 1.3 73.8 + - - +
42Q CYS 4.9 0.4 - - - +
151Q THR* 5.7 5.2 - - + -
194Q ASP* 4.8 12.3 - - - +
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Residues in contact with VAL 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q VAL* 3.1 21.7 + - + +
34Q ALA* 4.6 3.1 - - - -
35Q SER* 4.0 14.1 - - - +
39Q ALA* 1.3 84.3 - - - +
42Q CYS* 1.3 83.4 + - + +
58Q CYS* 4.4 10.8 - - + +
60Q ARG* 3.1 43.1 - - + +
194Q ASP* 4.2 13.7 + - - +
195Q SER* 5.0 3.8 + - - +
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Residues in contact with CYS 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q LEU* 3.4 24.6 - - - +
33Q VAL* 3.3 23.0 + - + -
41Q VAL* 1.3 92.2 + - + +
43Q GLY* 1.3 63.4 + - - +
54Q THR* 4.0 6.3 - - + +
57Q HIS* 4.8 3.4 - - - -
58Q CYS* 2.1 56.3 - - - -
194Q ASP* 3.9 14.0 + - - +
195Q SER* 3.6 15.7 - - - +
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Residues in contact with GLY 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q GLN* 5.4 2.9 - - - -
31Q VAL 3.5 15.3 - - - -
32Q LEU* 4.9 0.9 - - - -
33Q VAL* 4.6 5.2 - - - -
42Q CYS* 1.3 76.1 - - - +
44Q GLY* 1.3 58.4 + - - -
54Q THR* 2.9 22.4 + - - -
141Q TRP* 5.8 1.3 - - - -
194Q ASP* 5.4 2.2 - - - -
195Q SER 3.2 9.0 + - - -
196Q GLY* 3.8 13.0 - - - -
197Q GLY* 4.6 6.3 - - - -
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Residues in contact with GLY 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q TRP 3.8 1.4 - - - +
30Q GLN* 3.9 11.8 + - - +
31Q VAL* 3.5 35.7 + - - +
43Q GLY* 1.3 74.6 - - - -
45Q VAL* 1.3 73.0 + - - +
52Q VAL* 4.4 2.9 - - - -
53Q LEU 3.5 12.8 - - - -
54Q THR* 4.3 3.6 - - - -
196Q GLY 5.1 3.6 - - - -
198Q PRO* 4.5 1.7 - - - +
212Q ILE* 6.5 0.2 - - - -
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Residues in contact with VAL 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q TRP* 3.4 20.0 - - + +
44Q GLY* 1.3 81.3 - - - +
46Q LEU* 1.3 66.5 + - - +
47Q VAL* 3.5 11.2 + - + +
52Q VAL* 3.3 12.0 - - - +
53Q LEU* 3.2 34.0 + - + +
121Q MET* 3.5 34.3 - - + +
196Q GLY 5.8 0.4 - - - +
198Q PRO* 3.4 33.9 - - + -
209Q LEU* 4.4 12.6 - - + -
212Q ILE* 4.8 4.7 - - + -
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Residues in contact with LEU 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q PRO 5.5 0.4 - - - +
29Q TRP* 3.0 15.7 + - - +
31Q VAL* 4.7 2.5 - - + -
45Q VAL* 1.3 71.7 - - - +
47Q VAL* 1.3 53.1 + - - +
48Q HIS 3.7 8.1 - - - +
49Q PRO* 4.3 10.5 - - + +
51Q TRP 3.0 22.7 - - - +
52Q VAL* 3.3 14.9 - - + +
67Q LEU* 3.6 28.0 - - + -
108Q LEU* 5.2 3.6 - - + -
112Q ALA* 4.7 7.0 - - + -
114Q LEU* 4.8 4.7 - - + -
118Q VAL* 4.0 18.8 - - + -
119Q LYS 3.7 18.0 - - - +
120Q VAL* 3.3 14.4 - - + -
121Q MET* 2.7 35.3 + - - +
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Residues in contact with VAL 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q VAL* 3.6 17.5 - - + +
46Q LEU* 1.3 77.6 - - - +
48Q HIS* 1.3 78.4 + - + +
49Q PRO* 4.5 0.2 - - - +
51Q TRP* 3.5 20.4 + - + +
52Q VAL* 5.3 1.1 - - - -
53Q LEU* 4.7 19.5 - - + -
105Q LEU* 5.4 3.4 - - + -
120Q VAL* 3.0 23.8 - - - +
121Q MET 3.7 21.0 + - - +
122Q ASP* 5.4 2.8 - - - -
123Q LEU* 5.4 15.9 - - + -
209Q LEU* 5.5 5.2 - - + -
238Q ILE* 5.4 11.7 - - + -
242Q ILE* 4.6 6.1 - - + -
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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