Contacts of the strand formed by residues 133 - 144 (chain H) in PDB entry 1PPB
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 GLY 133 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H ALA* 1.3 71.3 - - - +
134H TYR* 1.3 67.1 + - - +
135H LYS* 3.6 3.8 + - - +
161H PRO* 3.8 14.7 - - - +
162H ILE 2.7 16.9 + - - -
14L SER* 4.0 10.4 - - - +
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Residues in contact with TYR 134 (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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129H LEU* 3.0 38.4 - - - +
131H GLN* 2.9 56.7 + - + +
132H ALA 4.4 4.3 - - - -
133H GLY* 1.3 77.4 - - - +
135H LYS* 1.3 60.3 + - - +
161H PRO* 3.4 0.2 - - - +
162H ILE* 2.9 30.9 + - + +
201H MET* 4.2 2.5 - - + -
14L SER* 3.4 89.9 + + - -
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Residues in contact with LYS 135 (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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133H GLY 4.3 1.8 - - - +
134H TYR* 1.3 73.1 - - - +
136H GLY* 1.3 58.9 + - - +
159H ASN 4.7 2.9 - - - +
160H LEU 3.5 4.9 - - - +
161H PRO* 3.8 22.2 - - + -
184H TYR* 2.9 30.6 - - - +
186H LYS* 4.1 9.1 - - - +
201H MET* 3.4 9.3 - - - +
14L SER* 2.9 115.7 + - + +
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Residues in contact with GLY 136 (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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134H TYR 4.0 0.2 + - - -
135H LYS* 1.3 73.3 - - - +
137H ARG* 1.3 58.9 + - - -
159H ASN* 3.1 6.9 - - - -
160H LEU 2.9 30.9 + - - -
199H PHE* 3.6 21.7 - - - -
200H VAL 3.3 14.4 - - - -
201H MET* 3.8 3.1 - - - -
14L LEU* 3.3 11.3 - - - +
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Residues in contact with ARG 137 (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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26H MET* 4.3 13.1 + - - +
27H SER* 6.2 1.1 - - - -
29H TRP* 6.3 0.4 - - - -
136H GLY* 1.3 72.7 - - - +
138H VAL* 1.3 67.6 + - - +
139H THR* 4.5 9.6 - - + -
157H VAL* 3.5 26.5 - - + +
158H VAL 3.1 7.0 - - - +
159H ASN* 3.5 19.4 + - - +
160H LEU 4.9 0.2 - - - +
198H PRO 3.3 1.9 - - - +
199H PHE* 3.1 7.9 - - - -
200H VAL* 2.9 46.9 + - + +
207H TRP* 3.1 32.9 - - + -
4L ARG* 3.8 6.7 - - - +
14L LEU* 2.8 71.3 + - + +
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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
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16H ILE* 3.8 22.2 - - + +
137H ARG* 1.3 70.4 - - - +
139H THR* 1.3 66.1 + - - +
156H GLN 3.7 0.9 - - - +
157H VAL* 3.5 2.8 - - - -
158H VAL* 2.7 45.8 + - + +
160H LEU* 4.6 6.3 - - + +
190H ALA* 4.5 4.3 - - + +
198H PRO 3.6 6.7 - - - +
199H PHE* 3.4 33.9 - - + -
213H VAL* 3.4 31.0 - - + -
228H TYR* 3.6 18.8 - - + +
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Residues in contact with THR 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ILE* 4.3 3.8 - - - -
22H ALA* 5.6 0.2 - - + -
26H MET* 5.8 1.3 - - - -
27H SER* 3.5 26.6 + - - +
29H TRP* 5.2 0.2 + - - -
30H GLN* 2.7 33.9 + - - +
137H ARG* 4.5 9.8 - - + +
138H VAL* 1.3 83.7 - - - +
140H GLY* 1.3 57.3 + - - +
155H LEU* 4.1 11.0 - - + -
156H GLN 3.2 9.6 - - - +
157H VAL* 4.2 21.8 - - + -
194H ASP* 4.6 2.8 - - - +
197H GLY* 4.2 10.9 - - - -
198H PRO* 3.8 12.7 + - - +
200H VAL* 5.7 2.6 - - + +
213H VAL* 5.2 0.2 - - - +
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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* 3.7 4.1 - - - +
30H GLN* 3.9 8.1 - - - -
139H THR* 1.3 74.8 - - - +
141H TRP* 1.3 61.7 + - - -
142H GLY 3.4 3.4 + - - -
155H LEU* 3.5 14.8 - - - +
156H GLN* 2.9 37.9 + - - +
193H GLY 5.7 0.2 - - - -
194H ASP* 3.4 14.8 - - - -
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Residues in contact with TRP 141 (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* 3.5 39.7 - - + -
31H VAL 3.9 7.0 - - - -
32H MET* 3.7 40.4 - - + -
40H LEU* 3.8 29.5 - - + +
42H CYS 5.4 1.6 - - - -
43H GLY* 5.4 2.0 - - - -
67H ARG 5.4 0.4 - - - -
70H LYS* 3.5 41.7 - - + -
71H HIS 2.9 23.3 + - - -
73H ARG* 3.6 34.2 - - + +
140H GLY* 1.3 72.2 - - - -
142H GLY* 1.3 62.0 + - - +
152H PRO* 3.6 16.0 - - + +
154H VAL 4.0 3.8 - - - -
155H LEU* 3.4 27.2 - - + +
193H GLY 4.8 6.1 + - - -
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Residues in contact with GLY 142 (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 3.4 6.9 + - - +
140H GLY 3.4 2.2 + - - -
141H TRP* 1.3 78.9 - - - +
143H ASN* 1.3 72.5 + - - +
144H LEU* 3.4 0.9 + - - +
151H GLN* 5.4 0.7 - - - -
152H PRO* 3.3 20.6 - - - +
192H GLU 3.6 9.2 - - - -
193H GLY* 3.8 12.5 + - - -
194H ASP* 3.2 18.6 + - - -
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Residues in contact with ASN 143 (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 2.7 30.0 + - - +
142H GLY* 1.3 73.1 - - - -
144H LEU* 1.3 56.6 + - - +
145H LYS 3.3 17.1 + - - +
147H THR* 3.1 28.3 + - - +
150H GLY 3.2 6.3 - - - +
151H GLN* 3.3 23.9 + - - -
191H CYS* 3.5 16.9 - - - +
192H GLU* 2.9 40.1 + - - +
193H GLY* 5.6 0.7 - - - -
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Residues in contact with LEU 144 (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 3.3 17.7 - - - +
17H VAL* 3.6 23.2 - - - +
18H GLU 4.9 0.7 + - - -
142H GLY 4.1 4.5 - - - +
143H ASN* 1.3 70.8 - - - +
145H LYS* 1.3 60.0 + - + +
149H LYS* 3.4 54.1 - - + +
150H GLY 2.8 13.7 + - - +
151H GLN 3.6 12.1 - - - +
152H PRO* 3.9 20.2 - - + -
156H GLN* 4.3 13.5 - - + +
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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