Contacts of the strand formed by residues 100 - 107 (chain A) in PDB entry 2E8A
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ARG 5.1 4.0 - - - +
77A LYS* 4.6 18.6 - - + +
78A PHE* 4.2 2.2 - - - -
95A ILE 3.6 0.2 - - - +
97A ASP* 2.9 36.0 + - - +
98A GLY 3.0 9.2 - - - +
99A ASP* 1.3 83.4 - - - +
101A PRO* 1.3 71.1 - - + +
102A LYS* 3.7 0.3 + - - +
115A TYR* 4.1 26.2 - - + -
117A GLU* 4.8 10.1 + - - +
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Residues in contact with PRO 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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73A LEU* 4.2 22.9 - - + +
76A ARG 3.1 25.4 - - - +
77A LYS 4.8 0.9 - - - -
78A PHE* 3.7 19.2 - - + +
83A VAL* 4.4 5.8 - - + -
94A VAL* 3.9 19.1 - - + -
95A ILE 3.4 7.0 - - - +
100A LYS* 1.3 86.7 - - + +
102A LYS* 1.3 63.4 + - - +
115A TYR* 3.9 2.6 - - - -
116A PRO* 3.2 36.4 - - + +
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Residues in contact with LYS 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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94A VAL* 3.3 4.5 - - - -
95A ILE* 2.8 40.9 + - + +
97A ASP* 3.5 35.6 + - + +
101A PRO* 1.3 81.3 - - - +
103A VAL* 1.3 64.0 + - - +
113A ALA* 3.6 38.0 + - + +
114A PHE 3.2 5.6 - - - +
115A TYR* 3.6 55.3 + - + +
116A PRO* 4.9 0.4 - - - -
118A GLU* 4.7 1.2 + - - -
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Residues in contact with VAL 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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67A VAL* 3.5 44.4 - - + -
70A ALA* 6.2 1.6 - - + -
73A LEU* 3.9 27.6 - - + -
92A PHE* 3.7 23.8 - - + -
93A GLN 3.4 5.2 - - - +
94A VAL* 4.5 2.0 - - + +
102A LYS* 1.3 73.6 - - - +
104A GLN* 1.3 59.9 + - - +
105A VAL* 4.0 9.7 + - + +
112A LYS 3.9 0.5 - - - +
113A ALA* 3.1 2.6 - - - -
114A PHE* 2.8 40.0 + - + +
116A PRO* 5.8 3.4 - - + -
119A ILE* 4.8 12.6 - - + -
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Residues in contact with GLN 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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64A GLN 4.6 1.9 - - - +
93A GLN* 2.8 53.5 + - + +
95A ILE* 4.1 34.8 - - + +
102A LYS 3.7 0.8 + - - -
103A VAL* 1.3 71.3 - - - +
105A VAL* 1.3 67.2 + - - +
111A THR* 3.5 32.8 - - + +
112A LYS 3.4 7.9 - - - +
113A ALA* 4.1 5.4 - - + +
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Residues in contact with VAL 105 (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 PHE* 3.7 27.4 - - + -
64A GLN 4.0 13.0 - - - +
65A ASN* 3.5 16.4 - - + +
67A VAL* 3.9 28.3 - - + -
103A VAL* 4.0 7.2 - - + +
104A GLN* 1.3 82.1 - - - +
106A SER* 1.3 66.3 + - - +
107A TYR* 4.5 2.7 - - + -
111A THR* 3.4 7.5 - - - +
112A LYS 2.8 37.9 + - - +
114A PHE* 4.0 14.8 - - + -
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Residues in contact with SER 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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44A PHE* 3.6 13.9 - - - +
45A THR 4.6 1.9 - - - +
46A ASP* 5.1 4.7 + - - -
65A ASN* 2.9 35.9 + - - -
105A VAL* 1.3 72.2 - - - +
107A TYR* 1.3 61.7 + - - +
108A LYS 4.4 0.2 - - - -
109A GLY* 4.6 7.6 + - - -
110A GLU 3.3 15.8 + - - -
111A THR* 4.6 2.0 - - - +
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Residues in contact with TYR 107 (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 PHE* 3.8 28.7 - + + -
45A THR 3.6 10.5 - - - -
48A GLU 3.6 10.3 - - - -
49A ARG* 2.7 56.9 + - + +
105A VAL* 4.5 4.3 - - + -
106A SER* 1.3 75.8 + - - +
108A LYS* 1.3 104.9 + - + +
109A GLY 3.1 0.4 - - - -
110A GLU* 2.8 25.1 + - - +
112A LYS* 4.2 29.9 - - + +
114A PHE* 4.4 11.2 - + - -
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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