Contacts of the strand formed by residues 134 - 142 (chain L) in PDB entry 1A4J
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 THR 134 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149H LYS* 4.6 21.3 - - - +
150H ASP* 5.6 0.3 + - - -
129L GLN* 3.4 19.7 + - - +
130L LEU* 3.2 27.5 + - - +
132L SER* 3.3 19.8 + - - -
133L GLY* 1.3 81.0 - - - +
135L ALA* 1.3 63.5 + - - +
185L THR* 5.2 5.8 - - + -
186L LEU 3.8 9.6 - - - +
187L SER* 5.3 1.1 - - - -
188L LYS 4.4 2.0 - - - -
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Residues in contact with ALA 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L PRO* 3.9 17.0 - - + -
129L GLN* 3.9 0.4 - - - -
130L LEU* 3.9 6.1 - - + -
134L THR* 1.3 78.2 - - - +
136L SER* 1.3 63.8 + - - +
137L VAL* 4.0 1.7 + - - +
184L LEU 3.6 2.8 - - - +
185L THR* 3.7 1.2 - - - +
186L LEU* 3.0 40.4 + - + +
187L SER 4.4 0.7 - - - +
188L LYS* 4.6 0.2 - - - -
191L TYR* 3.6 37.7 - - + -
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Residues in contact with SER 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H LEU* 3.6 22.7 - - - +
149H LYS* 3.8 6.9 + - - +
123L PHE 4.3 0.2 - - - +
124L PRO 3.9 1.6 - - - +
125L PRO* 3.3 23.8 - - - +
129L GLN* 2.9 32.8 + - - +
135L ALA* 1.3 73.2 - - - +
137L VAL* 1.3 62.6 + - - +
138L VAL* 4.1 3.4 + - - +
183L THR* 4.0 14.9 - - - +
184L LEU 3.5 4.3 - - - -
185L THR* 3.5 18.1 - - - +
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Residues in contact with VAL 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L ILE* 4.4 1.8 - - + -
123L PHE 3.3 15.3 - - - +
125L PRO* 4.1 14.1 - - + -
135L ALA 4.6 4.3 - - - +
136L SER* 1.3 78.5 - - - +
138L VAL* 1.3 59.7 + - - +
153L TRP* 3.5 29.4 - - + -
183L THR* 3.3 2.8 - - - -
184L LEU* 2.7 57.5 + - + +
186L LEU* 4.9 2.2 - - + -
191L TYR* 4.5 11.0 - - + -
197L TYR* 4.6 5.4 - - + -
214L PHE* 3.5 26.7 - - + -
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Residues in contact with VAL 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LEU* 4.6 22.0 - - + -
147H LEU* 4.6 21.1 - - + -
185H SER* 4.7 6.1 - - - +
187H VAL* 5.7 1.6 - - + -
122L ILE* 3.4 3.1 - - - +
123L PHE* 2.7 60.2 + - + +
136L SER 4.9 1.8 - - - +
137L VAL* 1.3 77.7 - - - +
139L CYS* 1.3 71.2 + - - +
140L LEU* 4.6 2.7 - - + +
153L TRP* 3.9 2.7 - - - -
181L SER* 4.6 12.6 - - - -
182L SER 3.5 5.8 - - - +
183L THR* 4.0 21.1 - - + +
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Residues in contact with CYS 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L VAL* 4.0 8.5 - - - -
121L PHE 3.4 3.1 - - - -
138L VAL* 1.3 74.4 - - - +
140L LEU* 1.3 61.1 + - - +
141L LEU* 3.9 13.3 + - - +
151L VAL* 3.8 12.3 - - - -
153L TRP* 3.4 19.5 - - + -
180L LEU 3.9 0.7 - - - +
181L SER* 3.3 4.0 - - - -
182L SER* 2.8 44.1 + - - +
199L CYS* 2.0 48.5 - - + -
201L VAL* 4.3 0.7 - - - -
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Residues in contact with LEU 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ALA* 5.5 4.3 - - - +
172H PHE* 4.0 14.1 - - + -
187H VAL* 3.9 38.4 - - + -
188H VAL 6.3 0.7 - - - -
189H THR* 5.6 3.1 - - + -
119L SER 3.2 5.0 - - - +
120L VAL* 3.3 3.8 - - - +
121L PHE* 2.7 66.9 + - + +
123L PHE* 4.1 17.3 - - + -
138L VAL* 4.1 3.1 - - + -
139L CYS* 1.3 73.2 - - - +
141L LEU* 1.3 72.0 + - - +
142L ASN* 3.8 22.9 - - - +
180L LEU 3.6 10.3 - - - +
181L SER* 4.6 1.3 - - - +
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Residues in contact with LEU 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118L PRO* 3.9 11.9 - - + -
119L SER 3.6 2.9 - - - -
120L VAL* 4.8 0.9 - - + -
139L CYS* 3.9 12.6 - - - +
140L LEU* 1.3 80.6 - - - +
142L ASN* 1.3 59.5 + - - +
144L PHE* 3.4 17.1 - - + -
149L ALA* 3.8 19.7 - - + -
151L VAL* 3.4 30.5 - - + -
179L SER* 3.3 6.9 - - - -
180L LEU* 2.8 47.1 + - + +
201L VAL* 3.3 46.7 - - + -
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Residues in contact with ASN 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H GLY 5.1 0.2 - - - +
170H HIS* 3.9 11.1 + - - -
187H VAL* 4.7 2.8 - - - +
189H THR* 3.5 34.4 + - - +
118L PRO* 3.4 3.2 - - - +
119L SER* 2.8 50.4 + - - +
121L PHE* 4.4 5.4 - - + -
140L LEU* 3.8 20.3 - - + +
141L LEU* 1.3 72.1 - - - +
143L ASN* 1.3 95.7 + - - +
144L PHE 3.6 0.9 - - - -
179L SER* 3.4 11.0 + - - -
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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