Contacts of the strand formed by residues 139 - 148 (chain H) in PDB entry 1I3R
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 ASN 139 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H THR 5.1 4.7 - - - +
131H LYS 4.9 8.5 - - - +
134H PRO* 5.1 13.6 - - - +
138H HIS* 1.3 77.2 - - - +
140H LEU* 1.3 61.0 + - - +
141H LEU 4.2 0.2 + - - -
187H LEU 3.7 0.2 - - - +
188H GLU* 3.7 3.3 - - - -
189H THR* 2.6 33.7 + - - +
190H VAL* 3.7 27.3 - - - +
191H PRO* 3.2 30.8 + - + +
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Residues in contact with LEU 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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309E NAG 6.2 2.9 - - + -
129H PRO* 3.4 5.7 - - - +
130H THR* 3.2 47.1 + - - +
131H LYS* 4.9 14.1 - - + +
138H HIS 3.8 2.6 + - - +
139H ASN* 1.3 76.1 - - - +
141H LEU* 1.3 61.7 + - - +
142H VAL 3.9 0.4 - - - -
169H VAL* 5.8 1.1 - - + -
186H MET* 3.3 49.8 - - + -
187H LEU 3.6 10.8 - - - +
188H GLU* 3.2 40.2 - - + +
191H PRO* 5.8 0.2 - - - -
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Residues in contact with LEU 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H VAL* 4.9 4.5 - - + -
128H TYR 4.2 0.9 - - - +
129H PRO* 4.0 17.5 - - + -
139H ASN 4.2 0.2 + - - -
140H LEU* 1.3 70.7 - - - +
142H VAL* 1.3 61.6 + - - +
157H TRP* 3.3 24.3 - - + -
186H MET* 3.3 2.3 - - - -
187H LEU* 2.9 47.6 + - + +
189H THR* 4.9 4.5 + - - +
191H PRO* 4.0 14.6 - - + -
197H TYR* 3.5 50.5 - - + -
214H TRP* 3.7 37.2 - - + -
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Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H VAL* 3.3 6.4 - - - +
128H TYR* 3.0 62.1 + - + +
130H THR* 3.7 30.3 - - + +
140H LEU* 4.6 0.9 - - + +
141H LEU* 1.3 73.6 - - - +
143H CYS* 1.3 71.1 + - - +
144H SER 4.0 0.4 + - - +
157H TRP* 4.0 1.6 - - - -
184H LEU* 4.1 22.0 - - + -
185H VAL 3.9 2.2 - - - -
186H MET* 3.3 31.0 - - + -
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Residues in contact with CYS 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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125H VAL* 4.0 14.6 - - - -
126H THR 3.4 12.3 - - - -
127H VAL* 4.5 0.4 - - - -
142H VAL* 1.3 73.9 - - - +
144H SER* 1.3 59.7 + - - +
145H VAL* 3.8 5.9 + - - +
155H VAL* 3.9 8.5 - - + -
157H TRP* 3.4 17.5 - - + +
183H THR 4.0 0.3 - - - +
184H LEU* 3.7 1.4 - - - -
185H VAL* 2.9 36.7 + - - +
199H CYS* 2.0 49.6 - - + -
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Residues in contact with SER 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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96G PRO* 3.4 27.2 - - - +
124H THR 3.4 1.7 + - - +
125H VAL* 3.2 7.6 - - - +
126H THR* 2.8 51.3 + - - +
128H TYR* 4.3 14.1 - - - -
142H VAL* 3.9 1.6 - - - -
143H CYS* 1.3 71.4 - - - +
145H VAL* 1.3 65.6 + - - +
146H SER* 4.1 1.4 + - - -
184H LEU* 3.6 24.5 - - - +
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Residues in contact with VAL 145 (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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123H PRO* 3.5 18.2 - - + -
124H THR 3.6 2.9 - - - -
125H VAL* 4.4 3.8 - - + -
143H CYS* 4.3 13.0 - - - +
144H SER* 1.3 76.3 + - - +
146H SER* 1.3 60.4 + - - +
148H PHE* 3.3 12.5 - - + -
153H ILE* 3.4 30.5 - - + -
155H VAL* 3.9 24.9 - - + -
183H THR* 2.8 46.4 + - + +
201H VAL* 4.1 15.9 - - + -
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Residues in contact with SER 146 (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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94G ARG 5.0 0.4 - - - -
95G SER* 4.2 9.0 - - - -
96G PRO* 3.2 36.3 - - - +
123H PRO* 3.4 2.9 - - - +
124H THR* 2.9 42.8 + - - +
144H SER* 4.1 1.5 + - - -
145H VAL* 1.3 76.1 - - - +
147H ASP* 1.3 69.3 - - - +
148H PHE* 3.5 3.6 - - - -
181H PHE 3.7 5.6 - - - -
182H GLN* 4.0 13.5 - - - +
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Residues in contact with ASP 147 (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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94G ARG* 2.8 42.5 + - - +
95G SER* 5.4 6.3 - - - -
121H VAL* 3.7 17.6 - - - +
122H GLU 3.1 18.6 - - - +
124H THR* 4.9 8.1 - - - +
146H SER* 1.3 81.0 - - - +
148H PHE* 1.3 55.9 + - - +
176H ASN* 5.2 1.9 - - - +
180H THR* 4.0 15.2 - - - +
181H PHE 3.0 11.7 + - - -
182H GLN* 4.6 1.0 - - - +
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Residues in contact with PHE 148 (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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121H VAL* 3.3 16.6 - - - +
123H PRO* 3.6 16.8 - - + -
145H VAL* 3.3 44.6 - - + -
146H SER 3.7 7.4 - - - -
147H ASP* 1.3 75.2 - - - +
149H TYR* 1.3 63.0 + - - +
150H PRO 3.3 18.4 - - - -
151H GLY 3.9 6.3 - - - -
153H ILE* 4.0 20.0 - - + -
173H LEU* 3.8 18.4 - - + -
180H THR* 3.4 3.4 - - - -
181H PHE* 2.8 60.9 + - + +
182H GLN* 3.8 2.9 - - - -
183H THR* 4.4 4.5 - - + -
203H HIS* 3.8 9.0 - - + -
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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