Contacts of the strand formed by residues 39 - 46 (chain H) in PDB entry 4IBL
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 ALA 39 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H LEU* 3.2 5.0 - - - -
35H VAL* 2.9 39.7 + - + +
37H ASN* 3.3 4.0 - - + +
38H GLY* 1.3 72.7 - - - -
40H GLN* 1.3 68.4 + - - +
41H LEU* 4.2 0.5 - - - +
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Residues in contact with GLN 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU* 3.9 18.1 - - + +
34H LEU* 3.7 14.2 - - + +
35H VAL* 5.8 0.5 - - - +
38H GLY 4.2 0.4 + - - -
39H ALA* 1.3 75.1 - - - +
41H LEU* 1.3 66.7 + - - +
42H CYS* 4.6 1.3 - - - +
73H LEU* 3.3 28.6 - - + +
141H TRP* 3.2 33.6 + - - +
142H GLY* 4.8 0.4 - - - -
151H THR* 4.4 19.1 + - - +
193H GLY* 4.3 13.3 + - - -
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Residues in contact with LEU 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU* 2.9 26.3 + - + +
35H VAL* 4.3 16.8 - - + +
39H ALA 3.3 0.4 + - - +
40H GLN* 1.3 80.2 - - - +
42H CYS* 1.3 75.7 + - + +
58H CYS* 3.5 29.2 - - + +
59H PHE* 4.4 11.4 - - + -
60H ILE* 3.9 17.3 - - - -
64H LEU* 3.8 29.2 - - + -
193H GLY* 5.2 5.1 - - - +
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Residues in contact with CYS 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU* 3.8 9.2 - - - +
33H LEU* 2.9 31.8 + - + +
40H GLN* 4.6 2.5 - - - +
41H LEU* 1.3 91.7 - - + +
43H GLY* 1.3 65.5 + - - +
57H HIS* 5.1 1.1 - - - -
58H CYS* 2.1 56.8 - - + -
141H TRP* 6.3 0.2 - - - -
192H LYS 5.2 1.3 - - - -
193H GLY 4.4 10.3 - - - -
195H SER* 3.4 15.3 - - - +
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Residues in contact with GLY 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H GLN* 3.8 10.1 - - - -
31H VAL 3.3 12.8 - - - -
32H LEU* 4.9 0.4 - - - -
33H LEU* 3.6 7.1 - - - +
42H CYS* 1.3 75.9 - - - +
44H GLY* 1.3 51.4 + - - -
54H SER* 2.8 27.4 + - - -
140H GLY* 6.2 1.1 - - - -
141H TRP* 5.6 2.2 - - - -
193H GLY 4.3 6.5 + - - -
194H ASP* 4.4 2.4 + - - -
195H SER 2.9 12.5 + - - +
196H GLY* 3.4 10.2 - - - -
197H GLY* 4.0 4.5 - - - -
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Residues in contact with GLY 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H GLN* 3.7 7.6 + - - +
31H VAL* 2.9 36.0 + - - -
33H LEU* 5.0 0.7 - - - -
43H GLY* 1.3 75.2 - - - -
45H THR* 1.3 65.3 + - - -
52H VAL* 4.2 3.8 - - - -
53H VAL 3.2 6.3 - - - -
54H SER* 4.2 4.7 - - - -
196H GLY 3.2 13.9 + - - -
198H PRO* 3.7 5.5 - - - +
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Residues in contact with THR 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H TRP* 3.5 8.3 - - + +
31H VAL* 3.8 4.4 - - - +
44H GLY* 1.3 76.8 - - - -
46H LEU* 1.3 75.1 + - - +
47H ILE* 3.5 8.1 + - + +
52H VAL* 3.3 1.7 - - - +
53H VAL* 2.8 41.3 + - - +
121H LEU* 3.7 33.0 - - + -
196H GLY 4.3 0.5 + - - -
197H GLY 4.0 1.2 - - - -
198H PRO* 3.1 30.7 - - + +
209H LEU* 3.9 16.6 - - + +
212H ILE* 6.1 0.3 - - - +
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Residues in contact with LEU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H TRP* 2.9 19.2 + - - +
31H VAL* 3.5 3.6 - - + +
45H THR* 1.3 77.0 - - - +
47H ILE* 1.3 58.5 + - - +
48H ASN 3.0 26.0 - - - +
49H THR 4.6 0.9 - - - -
51H TRP 3.8 9.6 - - - +
52H VAL* 4.0 13.2 - - + -
68H LEU* 3.8 26.9 - - + -
108H LEU* 4.6 7.2 - - + -
112H VAL* 3.9 29.4 - - + -
114H LEU* 4.3 3.8 - - + -
118H VAL* 4.1 5.8 - - + -
119H VAL 3.9 5.8 - - - -
120H PRO* 3.8 24.0 - - + -
121H LEU 2.8 24.6 + - - -
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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