Contacts of the strand formed by residues 91 - 101 (chain A) in PDB entry 5ELJ
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 LYS 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A VAL* 4.3 21.9 - - + +
84A GLU* 3.2 37.0 + - + +
85A ALA 3.6 4.9 - - - -
86A LYS* 4.2 26.5 - - + +
89A GLY 4.2 0.4 + - - -
90A LYS* 1.3 72.6 - - - +
92A LYS* 1.3 63.8 + - - +
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Residues in contact with LYS 92 (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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84A GLU* 3.3 5.1 - - - -
85A ALA 3.0 31.0 + - - +
87A ASP* 3.5 28.3 + - + -
90A LYS* 3.5 15.0 + - + +
91A LYS* 1.3 77.9 - - - +
93A LEU* 1.3 67.1 + - - +
94A TYR* 3.5 33.1 - - + +
120A PRO* 6.3 3.1 - - + -
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Residues in contact with LEU 93 (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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60A ARG* 5.3 2.2 - - - +
62A VAL* 4.1 21.8 - - + -
82A THR* 4.6 9.2 - - + -
83A LEU 3.3 11.2 - - - +
84A GLU* 3.9 25.1 - - + +
92A LYS* 1.3 76.6 - - - +
94A TYR* 1.3 68.1 + - - +
120A PRO* 3.7 4.0 - - - +
121A VAL* 3.3 46.2 + - + +
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Residues in contact with TYR 94 (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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48A HIS* 5.8 2.5 - + - -
56A LEU* 3.7 18.4 - - + +
81A LEU 3.7 0.5 - - - +
82A THR* 3.2 6.6 - - - +
83A LEU* 2.8 42.6 + - + +
85A ALA* 3.9 25.6 - - + -
87A ASP* 3.7 17.8 + - - +
92A LYS* 3.5 50.3 - - + +
93A LEU* 1.3 78.7 - - - +
95A GLU* 1.3 62.9 + - - +
118A PHE* 3.5 35.0 - + + -
119A LYS 3.4 5.6 - - - +
120A PRO* 3.9 30.7 - - + -
121A VAL* 4.2 2.7 - - - -
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Residues in contact with GLU 95 (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 LEU 3.4 3.6 - - - +
82A THR* 3.9 18.4 + - - +
94A TYR* 1.3 72.8 - - - +
96A ALA* 1.3 61.3 + - - +
97A LYS* 5.7 1.1 - - - -
117A GLU* 4.0 1.7 - - - +
118A PHE* 3.4 2.8 + - - -
119A LYS* 2.9 61.5 + - + +
121A VAL* 3.8 29.0 - - + +
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Residues in contact with ALA 96 (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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44A ALA* 4.1 17.9 - - + -
79A TYR 3.6 1.4 - - - +
80A TYR* 3.6 2.8 - - - -
81A LEU* 2.8 44.6 + - + +
83A LEU* 4.5 5.4 - - + -
94A TYR 4.1 0.2 - - - -
95A GLU* 1.3 74.5 - - - +
97A LYS* 1.3 64.8 + - - +
98A VAL 4.2 0.4 - - - -
115A LEU* 4.3 1.3 - - + -
117A GLU 3.2 10.3 - - - +
118A PHE* 3.8 22.9 - - + -
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Residues in contact with LYS 97 (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 MET* 3.9 16.6 - - + -
79A TYR 3.3 4.9 - - - +
80A TYR* 3.8 31.2 - - + -
95A GLU* 5.7 1.3 - - + +
96A ALA* 1.3 78.1 - - - +
98A VAL* 1.3 62.5 + - - +
115A LEU* 3.6 4.0 - - - +
116A GLN* 2.9 31.9 + - + +
117A GLU* 2.8 52.8 + - + +
119A LYS* 6.1 2.5 - - - +
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Residues in contact with VAL 98 (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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40A LEU* 4.1 28.0 - - + +
43A PHE* 4.1 18.6 - - + -
44A ALA* 4.2 11.0 - - + -
77A THR 3.8 0.7 - - - +
78A MET* 3.5 5.7 - - - +
79A TYR* 2.8 44.4 + - + +
81A LEU* 4.1 23.1 - - + -
96A ALA* 4.9 0.2 - - + -
97A LYS* 1.3 79.9 - - - +
99A TRP* 1.3 70.9 + - - +
100A VAL* 3.9 3.5 + - + +
113A LYS* 4.8 1.3 - - + -
114A GLU 3.5 9.4 - - - +
115A LEU* 4.2 15.3 - - + -
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Residues in contact with TRP 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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75A VAL 5.8 0.2 - - - -
76A PHE* 3.3 49.1 - + + -
77A THR 3.6 3.1 - - - -
78A MET* 3.8 10.6 - - - +
97A LYS 4.1 0.4 + - - -
98A VAL* 1.3 73.5 - - - +
100A VAL* 1.3 62.5 + - - +
101A LYS* 3.5 41.7 - - + -
112A PHE* 3.6 17.0 - - - -
113A LYS* 3.2 5.4 - - - -
114A GLU* 2.8 57.5 + - + +
116A GLN* 3.5 35.2 - - + +
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Residues in contact with VAL 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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40A LEU* 4.2 6.3 - - + -
76A PHE* 3.5 3.6 - - - +
77A THR* 2.8 49.1 + - - +
79A TYR* 3.9 28.7 - - + -
98A VAL* 4.2 3.1 - - + +
99A TRP* 1.3 83.8 - - - +
101A LYS* 1.3 73.1 + - - +
102A GLY 3.6 0.6 - - - +
103A LEU 5.1 0.2 - - - +
104A THR* 4.6 19.1 - - - +
112A PHE 3.8 6.3 - - - +
113A LYS* 4.0 34.1 - - + +
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Residues in contact with LYS 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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74A TRP* 5.6 13.2 - - + -
75A VAL 5.0 2.5 - - - +
76A PHE* 4.5 0.2 - - - -
99A TRP* 3.5 28.1 - - + -
100A VAL* 1.3 81.0 - - - +
102A GLY* 1.3 67.6 + - - +
103A LEU 3.6 3.6 + - - +
108A LEU* 3.6 28.2 - - + +
112A PHE* 2.9 59.8 + - + +
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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