Contacts of the strand formed by residues 135 - 140 (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 PHE 135 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H VAL* 3.5 17.8 - - - -
134H ARG* 1.3 94.0 - - + +
136H SER* 1.3 67.1 + - - +
159H ASN* 3.3 32.1 - - - +
160H VAL 3.4 16.2 - - - -
161H PRO* 3.6 19.5 - - + -
184H TYR* 3.5 25.1 - + - -
201H THR* 4.6 1.7 - - - +
202H HIS* 5.1 1.9 + - - +
41T LYS 5.6 0.7 - - - -
42T SER* 3.4 38.1 - - - -
44T ASP* 4.6 0.6 + - - -
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Residues in contact with SER 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H VAL 4.9 3.1 + - - -
134H ARG 5.2 0.3 + - - -
135H PHE* 1.3 78.6 + - - +
137H LEU* 1.3 64.0 + - - +
159H ASN* 3.1 8.5 + - - +
160H VAL* 2.8 34.2 + - - +
162H ARG* 6.0 0.7 - - - +
199H HIS* 3.4 33.9 - - - -
200H ALA 3.1 13.5 - - - -
201H THR* 2.6 28.7 + - - +
207H TRP* 5.4 1.8 - - - -
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Residues in contact with LEU 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H GLU 6.2 0.4 - - - +
27H CYS* 5.8 3.6 - - - -
136H SER* 1.3 74.6 - - - +
138H VAL* 1.3 62.1 + - - +
139H SER* 6.1 0.2 - - - -
157H VAL* 3.9 23.1 - - + -
158H LEU 3.3 13.2 - - - +
159H ASN* 3.4 31.6 - - + +
198H PRO* 3.4 2.4 - - - +
199H HIS* 3.3 2.1 - - - -
200H ALA* 2.8 46.4 + - + +
207H TRP* 3.5 33.9 - - + -
138L ILE* 6.5 0.4 - - + -
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Residues in contact with VAL 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ILE* 3.9 11.3 - - + +
137H LEU* 1.3 76.7 - - - +
139H SER* 1.3 63.5 + - - +
157H VAL* 3.3 3.9 - - - +
158H LEU* 2.9 55.8 + - + +
160H VAL* 3.8 14.4 - - + -
190H SER* 4.3 3.4 - - - -
198H PRO 3.3 6.5 - - - +
199H HIS* 3.6 24.9 - - + -
213H VAL* 4.5 6.1 - - + -
228H TYR* 3.5 42.4 - - + +
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Residues in contact with SER 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ILE* 3.9 8.7 - - - +
27H CYS* 4.5 11.5 - - - +
29H TRP* 5.8 0.7 + - - -
30H GLN* 2.7 29.3 + - - +
137H LEU 5.5 0.5 + - - -
138H VAL* 1.3 77.6 - - - +
140H GLY* 1.3 60.1 + - - +
155H LEU* 4.3 5.2 - - - -
156H MET 3.1 14.4 - - - -
157H VAL* 4.1 12.8 - - - -
194H ASP* 4.2 10.6 - - - +
197H GLY* 4.2 14.0 - - - -
198H PRO* 3.5 18.9 + - - +
213H VAL* 4.7 1.6 - - - +
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Residues in contact with GLY 140 (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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16H ILE* 3.8 1.3 - - - +
30H GLN* 4.0 9.9 - - - -
43H GLY* 6.2 0.7 - - - -
139H SER* 1.3 77.1 - - - +
141H TRP* 1.3 59.3 + - - -
142H GLY 3.7 1.0 + - - -
155H LEU* 3.4 16.5 - - - +
156H MET* 2.9 37.0 + - - +
193H GLY 5.5 0.2 - - - -
194H ASP* 3.2 18.9 + - - +
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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