Contacts of the strand formed by residues 114 - 123 (chain B) in PDB entry 5LAL
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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B TYR* 5.0 1.8 - - - -
105B PHE 3.1 16.2 - - - -
106B TYR* 4.3 3.4 - - - -
107B ASP* 3.7 7.1 - - - +
113B ASN* 1.3 80.6 + - - +
115B TRP* 1.3 63.7 + - - +
116B PHE* 3.6 4.6 - - - -
136B ALA* 3.8 2.8 - - - -
137B ASP* 2.8 56.8 + - - +
139B MET* 3.8 6.3 - - - -
218B GLY 3.1 21.2 + - - -
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Residues in contact with TRP 115 (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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103B PHE* 3.8 22.9 - + - -
104B TYR* 3.1 5.4 - - - -
105B PHE* 2.9 71.0 + + + -
107B ASP* 3.7 9.6 - - - +
114B SER* 1.3 75.4 - - - +
116B PHE* 1.3 88.4 + - - +
117B SER* 3.8 10.8 - - - -
134B MET* 3.8 31.4 - - + -
135B GLY* 3.6 11.5 - - - -
136B ALA* 3.7 28.9 - - + +
137B ASP 4.2 0.7 - - - +
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 4.5 12.3 - + - -
82B PHE* 4.1 10.1 - + - -
103B PHE 3.5 7.0 - - - -
104B TYR* 3.6 38.6 - + + -
114B SER* 3.6 2.0 - - - -
115B TRP* 1.3 85.6 - - - +
117B SER* 1.3 60.0 + - - +
118B TYR* 4.0 24.5 - + + -
134B MET* 3.3 2.4 - - - -
135B GLY 2.9 32.3 + - - -
137B ASP* 3.4 33.7 - - + -
146B LEU* 3.8 17.5 - - + -
164B PHE* 4.1 17.9 - + - -
175B PHE* 4.4 6.3 - + - -
179B MET* 5.4 0.7 - - + -
218B GLY* 3.6 21.5 - - - -
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Residues in contact with SER 117 (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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102B GLY* 3.4 2.3 - - - -
103B PHE* 2.9 59.2 + - - +
115B TRP* 3.8 12.2 - - - -
116B PHE* 1.3 75.2 - - - +
118B TYR* 1.3 63.3 + - - +
133B ILE 3.3 10.5 + - - -
134B MET* 3.9 8.1 - - - +
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Residues in contact with TYR 118 (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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82B PHE* 3.6 17.0 - + + -
100B ALA* 4.0 15.9 - - + -
101B GLN 3.4 14.8 - - - +
102B GLY* 3.8 1.1 - - - -
116B PHE* 4.0 24.2 - + + -
117B SER* 1.3 80.9 + - - +
119B THR* 1.3 68.1 + - - +
120B LEU* 3.9 12.3 - - + -
131B LEU 3.9 0.2 - - - +
132B ASN* 3.5 3.6 - - - +
133B ILE* 2.9 81.6 + - + +
162B ALA* 4.4 1.0 - - - +
164B PHE* 3.2 36.6 - + - -
179B MET* 3.3 24.9 - - + +
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Residues in contact with THR 119 (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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99B ARG 3.5 1.2 - - - +
100B ALA* 3.3 2.6 - - - -
101B GLN* 2.8 36.0 + - - -
118B TYR* 1.3 78.0 - - - +
120B LEU* 1.3 63.6 + - - +
121B VAL* 3.7 15.4 + - + +
130B THR* 3.5 32.1 - - + +
131B LEU 3.2 5.2 - - - +
132B ASN* 2.6 24.4 + - - +
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Residues in contact with LEU 120 (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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45B PHE* 4.1 14.6 - - + -
86B ILE* 3.8 33.9 - - + -
98B ALA* 5.1 2.0 - - + -
99B ARG 3.3 2.2 - - - +
100B ALA* 3.9 14.1 - - + -
118B TYR* 3.9 8.9 - - + -
119B THR* 1.3 71.2 - - - +
121B VAL* 1.3 59.5 + - - +
122B PHE* 3.7 21.5 - - + -
130B THR* 3.1 8.5 - - - -
131B LEU* 2.8 36.9 + - + +
133B ILE* 3.7 28.5 - - + -
179B MET* 4.5 3.4 - - - -
181B ILE* 4.0 22.4 - - + -
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Residues in contact with VAL 121 (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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98B ALA* 3.3 5.4 - - - +
99B ARG* 2.8 35.5 + - + +
101B GLN* 3.8 33.9 - - - +
119B THR* 3.9 22.2 - - + +
120B LEU* 1.3 76.0 - - - +
122B PHE* 1.3 67.3 + - - +
123B ASN* 4.2 6.0 + - + -
129B GLY 3.8 2.9 - - - +
130B THR* 4.4 11.0 - - + -
216B EDO 4.1 2.9 + - - -
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Residues in contact with PHE 122 (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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43B PHE* 3.8 31.4 - + - -
45B PHE* 4.1 20.6 - + - -
97B VAL 3.8 8.5 - - - -
98B ALA* 3.7 18.4 - - + -
120B LEU* 3.7 32.3 - - + -
121B VAL* 1.3 74.9 - - - +
123B ASN* 1.3 61.3 + - - +
124B SER* 5.3 0.2 - - - +
127B HIS* 3.5 34.5 - + + +
128B LYS* 3.4 5.5 - - - +
129B GLY 2.9 37.7 + - - +
131B LEU* 4.1 8.7 - - + -
155B PHE* 3.4 24.2 - + + -
216B EDO 3.7 2.5 - - - +
219B GLY 4.4 7.4 - - - -
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Residues in contact with ASN 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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121B VAL* 4.2 6.9 + - + +
122B PHE* 1.3 74.4 - - - +
124B SER* 1.3 60.1 + - - +
127B HIS 3.8 1.3 - - - -
128B LYS* 3.0 28.6 + - + +
216B EDO 2.8 30.5 + - - +
1F NAG 1.6 85.1 + - + +
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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