Contacts of the strand formed by residues 179 - 191 (chain A) in PDB entry 4LML
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 LEU 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 4.1 0.2 - - - -
133A SER* 3.0 36.7 + - - +
137A ARG* 3.6 44.2 - - + +
138A ASN 4.6 5.2 - - - +
139A ILE* 5.4 3.4 - - + -
172A ASN* 3.2 41.5 - - + +
173A PHE 3.5 8.1 - - - +
174A ALA* 4.4 3.8 - - + +
178A ARG* 1.3 74.4 - - - +
180A GLU* 1.3 69.1 + - - +
181A SER* 4.5 2.5 - - - +
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Residues in contact with GLU 180 (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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76A ARG* 3.5 9.9 + - - -
130A ILE* 3.3 35.2 - - + +
131A VAL 3.1 9.2 - - - +
132A ARG* 3.2 55.8 + - + +
171A ALA 3.5 1.0 - - - +
172A ASN* 3.3 5.0 - - - -
173A PHE* 2.9 44.2 + - + +
175A LEU* 3.8 24.3 - - + +
178A ARG 4.0 0.6 + - - -
179A LEU* 1.3 78.6 - - - +
181A SER* 1.3 61.8 + - - +
41D PHE* 4.2 2.9 - - - -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU 3.4 1.9 - - - +
130A ILE* 3.0 6.3 - - - -
131A VAL* 3.0 36.6 + - - +
138A ASN 3.8 2.2 + - - -
139A ILE* 3.4 22.7 - - - +
140A VAL* 3.5 30.1 - - - +
170A PRO* 4.2 3.9 - - - +
171A ALA 3.6 3.1 - - - -
172A ASN* 2.7 23.7 + - - -
179A LEU* 4.6 0.4 - - - +
180A GLU* 1.3 72.3 - - - +
182A LYS* 1.3 59.7 - - - +
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Residues in contact with LYS 182 (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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78A VAL* 4.2 23.0 - - - +
128A TYR* 3.6 43.0 - - + -
129A LEU 3.3 3.8 - - - +
130A ILE* 3.5 18.4 - - + -
169A LYS 4.5 1.0 - - - +
170A PRO* 3.5 3.9 - - - +
171A ALA* 2.9 45.2 + - + +
173A PHE* 3.9 33.4 - - + -
181A SER* 1.3 73.3 - - - +
183A LEU* 1.3 66.7 + - - +
184A ASP* 4.4 0.8 + - + -
151D ASN* 4.6 5.8 - - - +
153D ASP* 3.8 20.4 + - - -
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Residues in contact with LEU 183 (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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19A THR* 3.6 24.9 - - + +
127A ILE 3.6 1.7 - - - +
128A TYR* 3.2 7.6 - - - +
129A LEU* 2.9 37.4 + - + +
140A VAL* 3.9 17.0 - - + +
141A LEU* 3.7 28.7 - - - +
142A ALA* 3.8 6.3 - - + +
167A VAL 3.3 24.7 - - - +
168A VAL 4.1 5.6 - - - +
169A LYS 3.9 1.8 - - - +
170A PRO* 3.7 28.9 - - + -
182A LYS* 1.3 78.3 - - - +
184A ASP* 1.3 60.3 + - - +
185A TYR* 3.8 13.7 - - + -
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Residues in contact with ASP 184 (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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126A HIS* 3.1 22.9 + - - +
127A ILE 4.0 1.1 - - - -
128A TYR* 3.5 29.8 + - + -
166A ALA 3.7 0.2 - - - -
167A VAL* 2.8 46.4 + - + +
169A LYS 5.5 0.6 + - - -
182A LYS* 5.7 0.9 - - + -
183A LEU* 1.3 75.6 - - - +
185A TYR* 1.3 74.8 + - - +
186A GLN* 3.4 19.7 + - - +
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Residues in contact with TYR 185 (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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19A THR* 2.7 28.7 + - - -
20A GLY* 3.1 17.8 + - - -
21A ILE* 3.8 31.4 - - + -
126A HIS* 3.5 1.6 - - - -
127A ILE* 2.9 53.3 + - + +
129A LEU* 4.2 18.8 - - + -
142A ALA* 4.3 5.2 - - + +
147A LYS* 4.0 10.0 - - + +
164A PHE* 3.7 25.6 - + + -
165A THR 3.5 6.7 - - - +
166A ALA* 3.6 26.0 - - + -
183A LEU* 4.4 17.0 - - + -
184A ASP* 1.3 81.9 - - - +
186A GLN* 1.3 60.6 + - - +
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Residues in contact with GLN 186 (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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124A THR* 4.1 10.3 + - - +
125A LEU 3.3 6.3 - - - +
126A HIS* 3.6 22.3 - - - +
163A SER 3.6 0.3 - - - +
164A PHE* 3.4 7.4 - - - -
165A THR* 2.9 52.5 + - + +
167A VAL* 3.4 19.5 - - + +
184A ASP* 3.4 24.8 + - - +
185A TYR* 1.3 79.6 - - - +
187A LEU* 1.3 61.0 + - - +
188A ARG* 3.8 17.1 + - + -
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Residues in contact with LEU 187 (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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23A LEU* 3.8 24.5 - - + -
26A CYS* 3.8 28.5 - - - -
36A PHE* 4.7 10.1 - - + -
124A THR* 3.6 0.7 - - - -
125A LEU* 2.8 62.8 + - + +
127A ILE* 5.9 4.6 - - + +
156A LEU* 4.5 10.1 - - + -
161A ILE* 4.0 22.2 - - + -
163A SER 3.8 9.2 - - - +
164A PHE* 3.8 14.3 - - + -
185A TYR 4.3 0.6 - - - -
186A GLN* 1.3 73.2 - - - +
188A ARG* 1.3 60.4 + - - +
189A ILE* 3.6 11.1 + - + -
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Residues in contact with ARG 188 (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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122A SER* 6.1 3.0 - - - -
123A GLN 3.7 6.2 - - - +
124A THR* 4.1 33.9 + - - +
161A ILE* 4.8 0.3 - - - +
162A GLU* 2.9 31.7 + - + +
163A SER* 2.9 34.5 + - - +
165A THR* 5.0 3.4 - - + -
186A GLN* 4.3 20.1 + - + +
187A LEU* 1.3 71.7 - - - +
189A ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 189 (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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29A LEU* 3.6 25.4 - - + -
122A SER* 3.6 4.3 - - - -
123A GLN* 2.8 38.6 + - + +
125A LEU* 3.7 14.6 - - + -
156A LEU* 3.6 15.3 - - + -
159A TRP* 3.4 28.3 - - + -
160A ASP 3.3 15.3 - - - +
161A ILE* 3.8 19.1 - - + -
162A GLU* 3.6 3.1 - - - -
187A LEU* 3.9 24.5 - - + +
188A ARG* 1.3 80.0 - - - +
190A SER* 1.3 60.3 + - - +
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Residues in contact with SER 190 (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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120A PHE 5.5 1.6 - - - -
121A ASP 4.1 3.8 - - - -
122A SER* 3.1 26.2 - - - -
159A TRP* 3.6 3.8 - - - -
160A ASP* 2.9 41.2 + - - +
162A GLU* 3.1 18.7 + - - -
189A ILE* 1.3 73.1 - - - +
191A ARG* 1.3 66.3 + - - +
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Residues in contact with ARG 191 (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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31A ASP* 2.4 39.2 + - - -
113A LEU* 5.8 0.6 - - - +
115A PHE* 4.2 7.9 - - - -
118A TYR* 3.5 23.2 - - - -
119A PRO 3.3 22.0 + - - +
120A PHE 5.1 3.0 + - - +
121A ASP* 3.0 44.0 + - - +
123A GLN* 4.9 0.8 - - - +
158A GLY 4.2 4.9 - - - +
159A TRP* 3.1 46.9 - - + +
160A ASP* 4.8 2.3 - - - +
190A SER* 1.3 79.1 + - - +
192A GLN* 1.3 74.3 + - - +
193A TYR* 3.5 15.1 + - - -
196A TYR* 3.9 22.9 + - + +
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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