Contacts of the strand formed by residues 44 - 50 (chain D) in PDB entry 4IGM
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 LYS 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D LEU* 3.4 6.4 - - - -
41D LYS* 3.2 27.7 + - - +
42D ASP 3.0 14.5 + - - +
43D GLY* 1.3 79.8 - - - -
45D VAL* 1.3 66.4 + - - +
46D PHE 3.4 0.3 + - - -
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Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LYS* 4.0 26.2 - - + +
39D LEU 3.7 6.1 - - - +
40D LEU* 3.9 16.4 - - + -
43D GLY 5.4 0.7 - - - +
44D LYS* 1.3 75.3 - - - +
46D PHE* 1.3 62.8 + - - +
47D ARG* 3.8 20.0 - - - +
48D VAL* 4.1 19.3 - - + -
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Residues in contact with PHE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D VAL* 6.2 1.8 - - + -
39D LEU* 2.8 28.6 + - + +
40D LEU 5.0 0.2 - - - -
41D LYS* 4.2 32.8 - - + +
44D LYS 3.4 2.8 + - - -
45D VAL* 1.3 73.6 - - - +
47D ARG* 1.3 94.5 + - + +
78D VAL* 4.0 26.2 - - + -
176D TRP* 3.7 28.7 - + - -
180D MET* 5.8 1.3 - - + -
191D TRP* 4.0 30.1 - + - -
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Residues in contact with ARG 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LYS* 3.5 2.9 - - - -
39D LEU* 2.8 39.2 + - + +
45D VAL* 3.5 4.0 - - - +
46D PHE* 1.3 117.9 - - + +
48D VAL* 1.3 72.4 + - - +
49D VAL* 4.0 9.8 + - + -
76D VAL* 4.3 9.1 - - - +
176D TRP* 6.1 1.2 - - - -
188D TRP* 5.3 7.5 - - - -
191D TRP* 4.0 25.8 - - - +
291D ASP* 5.7 0.4 + - - -
294D PHE* 3.8 59.0 - - - +
295D PRO* 5.2 6.7 - - - +
296D LEU* 6.3 1.4 - - - +
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D HIS* 4.8 8.1 - - + +
36D GLU* 4.6 15.0 - - + +
37D ALA 3.5 12.3 - - - +
38D LYS* 4.3 13.5 - - + -
45D VAL* 4.1 16.2 - - + -
47D ARG* 1.3 82.3 - - - +
49D VAL* 1.3 69.4 + - - +
50D ARG* 5.6 1.6 - - + +
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Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 5.7 0.2 - - + -
29D LEU* 4.4 13.7 - - + -
36D GLU* 3.6 3.3 - - - +
37D ALA* 2.9 48.8 + - + +
39D LEU* 4.8 11.9 - - + -
47D ARG* 4.0 13.6 + - + -
48D VAL* 1.3 82.2 - - - +
50D ARG* 1.3 68.8 + - - +
53D CYS* 3.8 28.9 - - + -
54D TRP* 4.7 3.4 - - + +
293D PRO* 5.9 0.7 - - + -
294D PHE* 3.8 29.8 - - + -
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Residues in contact with ARG 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LYS 5.7 1.0 + - - -
35D GLY 3.3 10.3 + - - +
36D GLU* 4.2 30.3 + - + +
48D VAL* 5.6 1.6 - - + +
49D VAL* 1.3 79.6 - - - +
51D GLU* 1.3 63.4 + - + +
52D ASN* 3.2 18.1 + - - +
53D CYS* 2.9 27.0 + - - +
54D TRP* 3.8 7.2 + - - -
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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