Contacts of the strand formed by residues 130 - 140 (chain A) in PDB entry 4LKC
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A GLN* 3.2 37.6 + - - +
126A LEU* 3.8 5.2 + - - -
128A SER* 3.5 9.2 + - - -
129A GLY* 1.4 80.3 + - - +
131A ALA* 1.3 67.5 + - - +
181A THR* 3.8 25.1 - - + -
182A LEU 3.5 12.3 - - - +
183A SER* 4.3 1.7 - - - +
184A LYS* 4.1 2.8 - - - +
158B LYS* 4.2 16.2 - - - +
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO* 3.9 9.6 - - + -
125A GLN* 4.0 1.8 - - - -
126A LEU* 3.7 21.8 - - + -
130A THR* 1.3 74.3 - - - +
132A SER* 1.3 60.9 + - - +
133A VAL* 4.1 2.6 + - + +
180A LEU 3.4 4.2 - - - +
181A THR* 3.6 1.4 - - - -
182A LEU* 2.6 42.2 + - + +
183A SER 4.5 1.6 - - - +
187A TYR* 3.7 28.5 - - + -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE 4.4 0.2 - - - +
120A PRO 4.1 1.2 - - - +
121A PRO* 3.3 23.3 - - - +
125A GLN* 2.7 35.5 + - - +
131A ALA* 1.3 71.7 + - - +
133A VAL* 1.3 61.6 + - - +
134A VAL* 4.1 3.5 + - - +
179A THR* 4.1 13.9 - - - +
180A LEU 3.4 5.6 - - - -
181A THR* 4.5 3.6 + - - +
139B LEU* 6.1 0.5 - - - +
156B LEU* 3.5 21.8 - - - +
158B LYS* 3.4 18.2 - - - -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 4.4 1.1 - - + -
119A PHE 3.4 15.9 - - - +
120A PRO* 4.4 0.4 - - + -
121A PRO* 4.1 12.1 - - + -
131A ALA 4.6 4.0 - - - +
132A SER* 1.3 76.2 - - - +
134A VAL* 1.3 58.7 + - - +
149A TRP* 3.3 31.1 - - + -
179A THR* 3.4 1.9 - - - -
180A LEU* 2.7 59.6 + - + +
182A LEU* 4.7 2.5 - - + -
187A TYR* 4.5 8.7 - - + -
193A TYR* 4.4 13.9 - - + -
210A PHE* 3.5 26.7 - - + -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 3.4 4.0 - - - +
119A PHE* 2.7 50.3 + - + +
132A SER 4.8 3.6 - - - +
133A VAL* 1.3 76.7 - - - +
135A CYS* 1.3 70.7 - - - +
136A LEU* 4.2 2.2 - - + -
149A TRP* 3.8 2.7 - - - -
177A SER* 4.7 9.2 - - - -
178A SER 3.4 7.4 - - - +
179A THR* 3.9 26.5 - - + +
139B LEU* 3.8 31.2 - - + -
156B LEU* 4.8 7.9 - - + -
194B SER* 4.3 17.5 - - - +
196B VAL* 5.9 2.2 - - + -
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Residues in contact with CYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A VAL* 3.8 20.0 - - - -
117A PHE 3.4 6.5 - - - -
118A ILE* 4.5 0.9 - - + +
134A VAL* 1.3 75.9 - - - +
136A LEU* 1.3 62.1 + - - +
137A LEU* 4.1 8.8 - - - +
149A TRP* 3.5 16.5 - - + -
176A LEU 3.7 0.7 - - - +
177A SER* 3.4 4.9 - - - -
178A SER* 2.8 41.2 + - - +
195A CYS* 2.0 49.6 - - + -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A SER 3.4 1.0 - - - +
116A VAL* 3.3 10.0 - - - +
117A PHE* 2.7 57.7 + - + +
119A PHE* 4.2 13.2 - - + -
134A VAL* 4.2 2.9 - - + -
135A CYS* 1.3 73.8 - - - +
137A LEU* 1.3 76.7 + - - +
138A ASN* 4.2 20.0 - - + +
175A SER* 4.8 0.9 - - - -
176A LEU 3.5 1.1 - - - -
177A SER* 4.8 0.9 - - - +
152B ALA* 3.9 16.4 - - + -
181B PHE* 3.7 31.2 - - + -
196B VAL* 3.9 32.3 - - + -
198B THR* 4.9 1.1 - - + -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PRO* 4.1 9.2 - - + -
115A SER 3.6 3.8 - - - -
116A VAL* 4.8 0.9 - - + -
135A CYS* 4.1 12.1 - - - +
136A LEU* 1.3 78.6 - - - +
138A ASN* 1.3 58.9 + - - +
140A PHE* 3.6 20.9 - - + -
145A ALA* 3.9 19.3 - - + -
147A VAL* 3.7 26.9 - - + -
175A SER* 3.2 7.1 - - - -
176A LEU* 2.7 51.4 + - + +
197A VAL* 3.6 48.0 - - + -
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ALA 4.4 0.5 - - - +
114A PRO* 3.5 1.7 - - - +
115A SER* 2.8 49.4 + - - +
117A PHE* 4.3 4.5 - - + -
136A LEU* 4.2 18.2 - - + +
137A LEU* 1.3 72.5 - - - +
139A ASN* 1.3 98.6 + - - +
140A PHE 3.8 0.4 - - - -
175A SER* 3.6 1.7 + - - -
179B HIS* 3.2 26.6 + - - -
196B VAL* 4.7 1.4 - - - +
198B THR* 3.8 30.7 + - - +
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Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA* 4.2 5.4 - - - +
113A ALA 3.8 9.2 - - - +
138A ASN* 1.3 96.6 - - - +
140A PHE* 1.3 57.8 + - - +
168A ASP* 5.4 1.0 - - - +
171A ASP* 4.4 10.5 + - - +
173A THR* 3.5 30.8 + - + +
174A TYR 3.3 6.0 + - - -
175A SER* 2.9 12.9 + - - -
177B GLY* 6.4 0.6 - - - -
179B HIS* 3.0 27.6 + - - -
198B THR* 5.1 2.2 + - - -
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA* 3.3 13.9 - - - +
114A PRO* 3.6 32.5 - - + -
137A LEU* 3.6 33.2 - - + -
139A ASN* 1.3 74.4 - - - +
141A TYR* 1.4 63.1 + - - +
142A PRO 3.3 19.7 - - - -
143A ARG* 3.4 28.9 - - - -
145A ALA* 4.1 12.1 - - + -
164A VAL* 4.9 1.6 - - + -
173A THR* 3.5 4.2 - - - -
174A TYR* 2.8 63.2 + - + -
175A SER 4.5 0.2 - - - -
176A LEU* 3.6 28.5 - - + -
199A HIS* 3.4 10.5 - + - +
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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