Contacts of the strand formed by residues 122 - 132 (chain B) 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 SER 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B ASP* 5.2 4.0 - - - +
117B ARG* 5.6 3.2 - - - +
120B PHE 5.2 0.2 + - - -
121B ASP* 1.3 86.1 - - - +
123B GLN* 1.3 63.3 + - - +
124B THR* 5.9 0.3 - - - +
162B GLU* 5.1 0.5 + - - -
188B ARG* 5.3 11.2 - - - -
189B ILE 3.3 9.9 - - - -
190B SER* 3.1 21.2 - - - +
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PRO 4.0 2.6 - - - +
113B LEU* 3.1 31.0 - - + +
114B ASP* 2.7 41.5 + - - +
121B ASP* 2.0 33.5 + - - +
122B SER* 1.3 75.5 - - - +
124B THR* 1.3 65.6 + - - +
125B LEU* 4.0 1.3 - - + -
159B TRP* 3.4 31.2 - - + -
188B ARG* 3.6 5.2 - - - +
189B ILE* 2.8 40.4 + - + +
191B ARG* 4.1 5.4 - - - +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B SER* 4.1 5.0 + - - -
112B PRO* 4.5 6.8 - - - +
122B SER 5.9 0.2 - - - +
123B GLN* 1.3 77.7 + - - +
125B LEU* 1.3 67.9 + - - +
126B HIS* 3.6 30.7 + - + +
186B GLN* 4.3 11.1 + - - +
187B LEU 3.5 4.5 - - - -
188B ARG* 3.7 43.5 + - - +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.9 9.9 - - + -
36B PHE* 3.6 51.1 - - + -
111B SER* 3.6 9.4 - - - +
112B PRO 4.5 0.2 - - - +
113B LEU* 3.6 31.2 - - + -
123B GLN* 4.8 3.1 - - + -
124B THR* 1.3 77.1 + - - +
126B HIS* 1.3 62.4 + - - +
127B ILE* 5.4 0.8 - - + +
156B LEU* 4.4 1.1 - - + -
185B TYR 3.6 0.2 - - - +
186B GLN* 3.3 7.3 - - - -
187B LEU* 2.9 52.6 + - + +
189B ILE* 3.7 26.5 - - + -
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Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 4.5 0.3 - - - -
79B ASN* 2.8 20.5 + - - +
109B VAL* 3.2 11.4 - - - +
111B SER* 2.9 18.3 + - - +
112B PRO* 4.6 13.0 - - + +
124B THR* 3.6 25.3 + - + +
125B LEU* 1.3 81.9 - - - +
127B ILE* 1.3 65.1 + - - +
128B TYR* 3.1 36.1 + - + -
184B ASP* 3.3 25.9 + - - +
185B TYR 3.4 1.1 - - - -
186B GLN* 3.9 15.3 + - + -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.8 8.5 - - + -
23B LEU* 5.2 2.0 - - + -
36B PHE* 3.9 17.7 - - + -
38B VAL* 4.3 16.2 - - + -
77B PHE* 3.3 37.0 - - + -
79B ASN* 3.9 2.9 - - - +
105B PHE* 5.8 1.1 - - + -
109B VAL* 3.8 26.9 - - + -
125B LEU 5.4 1.1 - - - -
126B HIS* 1.3 80.8 - - - +
128B TYR* 1.3 62.1 + - - +
129B LEU* 4.2 5.2 - - + -
164B PHE* 5.0 16.8 - - + -
183B LEU 3.6 1.0 - - - +
184B ASP* 4.4 0.2 + - - -
185B TYR* 2.9 44.7 + - + +
187B LEU* 6.2 2.7 - - + +
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Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PHE* 3.4 8.5 - - - +
78B VAL* 3.0 46.6 + - + -
79B ASN* 3.1 33.9 + - + +
112B PRO* 6.2 2.2 - - + -
126B HIS* 3.1 42.3 + - + -
127B ILE* 1.3 74.4 - - - +
129B LEU* 1.3 64.6 + - - +
182B LYS* 3.8 30.7 - - + -
183B LEU 3.2 11.9 - - - +
184B ASP* 3.3 32.8 + - + -
153C ASP* 5.5 5.6 + - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR* 4.3 16.2 - - + -
21B ILE* 4.2 7.4 - - + -
42B LEU* 4.1 24.2 - - + -
44B LEU* 5.7 0.2 - - + -
75B ILE* 4.2 18.8 - - + -
76B ARG 3.6 3.4 - - - +
77B PHE* 3.5 39.5 - - + -
127B ILE* 4.2 7.4 - - + -
128B TYR* 1.3 78.4 - - - +
130B ILE* 1.3 61.8 + - - +
140B VAL* 4.2 5.1 - - + +
181B SER 3.3 2.1 - - - +
182B LYS* 3.2 3.2 - - - -
183B LEU* 2.9 43.1 + - + +
185B TYR* 4.0 23.3 - - + -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE* 3.6 6.3 - - - +
76B ARG* 2.9 77.3 + - - +
78B VAL* 3.5 29.6 - - + +
129B LEU* 1.3 73.7 - - - +
131B VAL* 1.3 63.9 + - - +
140B VAL* 5.2 0.9 - - - -
173B PHE* 5.6 2.5 - - + -
175B LEU* 6.5 0.4 - - + -
180B GLU* 3.4 16.2 - - + +
181B SER 3.0 6.7 - - - +
182B LYS* 3.5 31.2 - - + -
24C ILE* 6.1 2.5 - - + -
41C PHE* 5.3 2.7 - - + -
104C ARG* 4.3 5.4 - - - +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 5.7 0.4 - - + -
73B PRO* 4.7 1.3 - - + -
74B GLU 3.6 21.8 - - - +
75B ILE* 3.7 19.5 - - + -
76B ARG* 5.6 2.0 - - - +
130B ILE* 1.3 76.7 - - - +
132B ARG* 1.3 70.4 + - - +
138B ASN* 4.0 28.9 - - + +
140B VAL* 3.5 27.4 - - + +
179B LEU 4.1 0.2 - - - +
180B GLU* 3.1 9.2 - - - -
181B SER* 2.9 43.5 + - - +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLU* 4.3 7.4 + - - +
76B ARG* 4.8 6.1 - - - +
131B VAL* 1.3 85.2 - - - +
133B SER* 1.3 70.4 + - - +
134B VAL* 5.2 1.9 - - - +
138B ASN* 4.3 4.4 + - - +
175B LEU* 2.8 22.0 + - - +
176B GLU* 3.0 29.1 + - - +
178B ARG* 3.3 31.2 - - + +
179B LEU 3.8 2.5 - - - +
180B GLU* 3.1 39.7 + - + +
41C PHE* 4.9 3.2 - - - -
89C VAL* 3.8 26.3 - - + +
90C ASP* 5.3 4.7 - - - +
102C LEU* 3.5 24.4 - - - +
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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