Contacts of the strand formed by residues 114 - 123 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A TYR* 4.9 1.6 - - - -
105A PHE 3.1 17.9 - - - -
106A TYR* 4.2 4.3 - - - -
107A ASP* 3.7 7.8 - - - +
113A ASN* 1.3 80.7 + - - +
115A TRP* 1.3 64.6 + - - +
116A PHE* 3.6 4.8 - - - -
136A ALA* 3.8 3.3 - - - +
137A ASP* 2.8 58.3 + - - +
139A MET* 3.8 5.4 - - - -
215A GLY* 3.2 16.9 + - - -
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Residues in contact with TRP 115 (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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103A PHE* 3.9 14.8 - + - -
104A TYR* 3.1 5.4 - - - -
105A PHE* 3.0 69.6 + + + -
107A ASP* 3.7 9.9 - - - +
114A SER* 1.3 76.8 - - - +
116A PHE* 1.3 88.9 + - - +
117A SER* 3.8 17.5 - - - -
134A MET* 4.0 28.9 - - + -
135A GLY* 3.6 22.9 - - - -
136A ALA* 3.9 15.5 - - + +
137A ASP 4.2 0.7 - - - +
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Residues in contact with PHE 116 (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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47A PHE* 4.4 12.1 - + - -
82A PHE* 4.0 11.9 - + - -
103A PHE 3.5 7.6 - - - -
104A TYR* 3.5 36.6 - + + -
114A SER* 3.6 7.0 - - - -
115A TRP* 1.3 88.8 - - - +
117A SER* 1.3 60.7 + - - +
118A TYR* 4.0 23.1 - + + -
134A MET* 3.2 1.6 - - - -
135A GLY 2.9 32.7 + - - +
137A ASP* 3.4 37.7 - - + -
146A LEU* 3.8 17.5 - - + -
164A PHE* 4.1 16.8 - + - -
175A PHE* 4.4 10.3 - + - -
177A VAL* 5.7 0.4 - - + -
179A MET* 5.5 0.4 - - + -
215A GLY* 3.7 10.8 - - - -
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Residues in contact with SER 117 (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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102A GLY* 3.4 2.1 - - - -
103A PHE* 2.9 59.1 + - - -
115A TRP* 3.8 10.6 - - - -
116A PHE* 1.3 74.3 - - - +
118A TYR* 1.3 62.9 + - - +
133A ILE 3.3 12.0 + - - -
134A MET* 3.6 13.0 - - - +
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Residues in contact with TYR 118 (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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82A PHE* 3.6 19.1 - + + -
100A ALA* 4.1 11.2 - - + -
101A GLN 3.3 13.7 - - - +
102A GLY* 3.9 0.9 - - - -
116A PHE* 4.0 22.7 - + + -
117A SER* 1.3 81.6 + - - +
119A THR* 1.3 75.2 + - - +
120A LEU* 3.9 16.6 - - + -
131A LEU 3.9 0.2 - - - +
132A ASN* 3.6 3.3 - - - +
133A ILE* 2.9 80.8 + - + +
146A LEU* 4.5 0.2 - - + -
162A ALA* 4.4 1.4 - - - +
164A PHE* 3.2 37.0 - + - -
179A MET* 3.3 21.3 - - + -
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Residues in contact with THR 119 (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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99A ARG 3.6 0.7 - - - +
100A ALA* 3.4 2.8 - - - -
101A GLN* 2.8 40.1 + - - -
118A TYR* 1.3 79.5 - - - +
120A LEU* 1.3 63.6 + - - +
121A VAL* 3.7 15.1 + - + +
130A THR* 3.5 32.1 - - + +
131A LEU 3.2 7.6 - - - +
132A ASN* 2.7 21.1 + - - +
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Residues in contact with LEU 120 (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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45A PHE* 4.0 19.7 - - + -
86A ILE* 3.8 35.2 - - + -
98A ALA* 5.1 2.2 - - + -
99A ARG 3.3 1.8 - - - +
100A ALA* 3.9 13.2 - - + -
118A TYR* 3.9 16.1 - - + -
119A THR* 1.3 71.2 - - - +
121A VAL* 1.3 61.0 + - - +
122A PHE* 3.8 16.5 - - + -
130A THR* 3.1 9.4 - - - -
131A LEU* 2.8 45.9 + - + +
133A ILE* 3.8 20.6 - - + -
179A MET* 4.4 3.1 - - - -
181A ILE* 3.9 18.8 - - + -
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Residues in contact with VAL 121 (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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98A ALA* 3.3 5.0 - - - +
99A ARG* 2.8 37.2 + - + +
101A GLN* 3.7 35.0 - - - +
119A THR* 3.9 23.1 - - + +
120A LEU* 1.3 74.2 - - - +
122A PHE* 1.3 68.8 + - - +
123A ASN* 4.1 5.4 + - + +
129A GLY 3.8 2.7 - - - -
130A THR* 4.3 12.1 - - + -
212A EDO 4.1 2.1 + - - -
1D NAG 5.0 13.2 - - + +
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Residues in contact with PHE 122 (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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43A PHE* 3.9 25.6 - + - -
45A PHE* 4.2 24.9 - + - -
97A VAL 3.8 15.0 - - - +
98A ALA* 3.8 13.7 - - + -
120A LEU* 3.8 25.8 - - + -
121A VAL* 1.3 76.4 - - - +
123A ASN* 1.3 63.1 + - - +
127A HIS* 3.4 35.7 - - + +
128A LYS* 3.3 2.9 - - - +
129A GLY 2.8 36.5 + - - +
131A LEU* 4.1 10.1 - - + -
155A PHE* 3.4 22.7 - + + -
212A EDO 3.7 3.1 - - - +
216A GLY 4.5 10.1 - - - -
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Residues in contact with ASN 123 (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 VAL* 4.1 6.7 + - + -
122A PHE* 1.3 74.4 - - - +
124A SER* 1.3 59.4 + - - +
127A HIS 3.7 1.1 - - - -
128A LYS* 4.0 19.8 + - - +
212A EDO 2.9 29.9 + - - +
1D NAG 1.5 73.0 + - + +
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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