Contacts of the strand formed by residues 98 - 106 (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 ALA 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ILE* 3.0 38.7 + - + +
96A PRO* 3.4 9.7 - - - +
97A VAL* 1.3 80.2 - - + +
99A ARG* 1.3 71.1 + - - +
120A LEU* 5.1 2.0 - - + -
121A VAL 3.3 18.4 - - - +
122A PHE* 3.8 26.0 - - + -
212A EDO 3.6 7.8 + - - -
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Residues in contact with ARG 99 (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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61A THR* 5.0 2.6 - - - +
83A ASP* 2.8 53.1 + - - +
84A GLY* 3.3 19.2 - - - +
85A PRO* 3.6 11.9 - - - +
86A ILE* 4.0 4.3 - - - -
96A PRO* 4.1 21.4 - - - +
98A ALA* 1.3 80.0 - - - +
100A ALA* 1.3 59.4 + - - +
101A GLN* 4.0 16.2 - - - +
119A THR 3.6 0.5 - - - +
120A LEU* 3.3 5.2 - - - +
121A VAL* 2.8 37.9 + - + +
212A EDO 3.7 13.0 - - - +
1D NAG 6.5 0.4 - - - -
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Residues in contact with ALA 100 (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* 3.7 31.4 - - + -
82A PHE* 3.3 12.5 - - + -
83A ASP* 3.3 3.1 - - - -
84A GLY 2.8 33.0 + - - -
86A ILE* 4.0 3.5 - - + +
99A ARG* 1.3 74.0 - - - +
101A GLN* 1.3 60.7 + - - +
118A TYR* 4.1 9.2 - - + -
119A THR 3.4 4.7 - - - -
120A LEU* 3.9 17.9 - - + -
179A MET* 5.1 0.4 - - + -
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Residues in contact with GLN 101 (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 3.3 5.6 - - - +
83A ASP* 3.2 39.8 + - + +
99A ARG* 4.0 17.3 - - + +
100A ALA* 1.3 71.3 - - - +
102A GLY* 1.3 58.7 + - - +
118A TYR* 3.3 3.2 - - - -
119A THR* 2.8 42.7 + - - +
121A VAL* 3.7 26.2 - - + +
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Residues in contact with GLY 102 (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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81A ILE* 3.5 8.7 - - - +
82A PHE* 2.9 37.3 + - - +
101A GLN* 1.3 76.3 - - - +
103A PHE* 1.3 65.9 + - - +
117A SER 3.4 11.0 - - - -
118A TYR* 3.8 3.1 - - - -
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Residues in contact with PHE 103 (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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79A PHE* 3.3 44.9 - + + -
80A VAL 3.1 14.8 - - - +
81A ILE* 4.1 5.8 - - + -
82A PHE* 3.4 11.2 - - - -
102A GLY* 1.3 77.3 - - - +
104A TYR* 1.3 64.0 + - - +
105A PHE* 3.9 13.9 - + - -
115A TRP* 3.9 23.3 - + - -
116A PHE* 3.5 3.3 - - - -
117A SER* 2.9 59.4 + - - +
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Residues in contact with TYR 104 (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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49A ASP* 2.9 35.3 + - - -
51A LEU* 3.9 10.9 - - - +
79A PHE* 3.7 1.4 - - - -
80A VAL* 2.8 71.8 + - + +
82A PHE* 3.6 17.9 - + - -
103A PHE* 1.3 75.8 - - - +
105A PHE* 1.3 71.8 + - - +
106A TYR* 3.9 26.6 + + - -
114A SER* 4.9 0.9 - - - -
115A TRP 3.1 13.7 - - - +
116A PHE* 3.5 29.6 - + + -
175A PHE* 3.5 17.0 - + - -
215A GLY* 4.2 10.5 - - - -
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Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLY* 4.9 4.3 - - - +
78A LYS 3.2 14.6 - - - +
79A PHE* 3.7 33.9 - + + -
103A PHE* 3.9 13.0 - + - -
104A TYR* 1.3 78.2 - - - +
106A TYR* 1.3 74.0 + - - +
107A ASP* 3.9 16.8 - - + -
114A SER* 3.1 6.1 - - - -
115A TRP* 3.0 77.9 + + + -
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Residues in contact with TYR 106 (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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51A LEU* 6.0 2.2 - - + +
74A PHE 4.0 4.0 - - - +
75A LYS* 3.3 33.9 - - + +
76A PHE* 4.1 1.0 - - - -
77A GLY* 2.8 25.8 + - - -
78A LYS* 3.1 41.6 + - + -
104A TYR* 3.9 26.9 + + - -
105A PHE* 1.3 76.6 - - - +
107A ASP* 1.3 64.9 + - - +
108A MET 4.0 0.7 - - - -
112A PHE* 4.4 17.9 - + - -
113A ASN 3.1 17.7 - - - +
114A SER* 4.2 2.0 - - - -
139A MET* 3.7 27.4 - - + +
175A PHE* 4.8 3.5 - - - -
215A GLY* 3.1 20.8 + - - -
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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