Contacts of the strand formed by residues 94 - 103 (chain H) in PDB entry 1E50
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 94 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87H ASP 3.8 6.2 - - - +
88H LEU* 3.9 11.8 - - - +
91H GLU* 3.0 58.7 + - + +
92H ALA 4.2 3.4 - - - +
93H GLY* 1.3 81.9 - - - +
95H VAL* 1.3 59.2 + - - +
96H TYR* 3.7 17.2 + - + -
113H TRP* 3.5 45.8 - - + +
114H ILE 2.9 23.1 - - - +
115H ASP* 3.9 7.0 - - + +
116H LEU* 3.6 8.8 - - - +
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Residues in contact with VAL 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H PHE* 3.9 33.7 - - + -
48H CYS* 4.4 6.1 - - + -
86H VAL* 3.9 16.2 - - + -
87H ASP 3.2 28.7 - - - +
88H LEU* 3.7 17.0 - - + -
94H LYS* 1.3 77.4 - - - +
96H TYR* 1.3 70.1 + - - +
97H LEU* 3.9 13.7 + - + +
113H TRP* 3.0 3.0 - - - -
114H ILE 2.9 28.8 + - - +
116H LEU* 3.9 5.6 - - + +
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Residues in contact with TYR 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H GLU 5.3 1.3 - - - +
85H TYR 3.6 1.7 - - - +
86H VAL* 3.6 4.5 - - - -
87H ASP* 3.0 43.6 + - + +
90H ARG* 3.4 64.9 + - + +
91H GLU* 2.6 40.3 + - + -
94H LYS* 3.7 13.3 + - + -
95H VAL* 1.3 79.4 - - - +
97H LEU* 1.3 59.2 + - - +
112H GLY 3.4 8.1 - - - +
113H TRP* 3.5 36.0 + + + -
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Residues in contact with LEU 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H PHE* 4.2 18.8 - - + -
48H CYS* 4.1 7.2 - - - -
55H ILE* 3.8 22.7 - - + -
68H PHE* 3.3 46.2 - - + -
84H GLU 5.4 0.2 - - - -
85H TYR 3.4 11.7 - - - +
86H VAL* 4.0 7.0 - - + -
95H VAL* 3.9 24.7 - - + +
96H TYR* 1.3 79.6 - - - +
98H LYS* 1.3 59.7 + - - +
110H TRP* 3.6 11.7 - - + +
111H LYS* 3.3 6.2 - - - +
112H GLY 2.6 33.9 + - - +
114H ILE* 4.9 4.0 - - + -
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Residues in contact with LYS 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H PHE* 3.1 16.2 - - - +
84H GLU* 2.9 50.2 + - + +
85H TYR* 3.1 48.9 + - + -
97H LEU* 1.3 75.4 - - - +
99H ALA* 1.3 63.2 + - - +
100H PRO* 6.0 0.4 - - - -
109H ILE* 3.7 37.2 - - + +
110H TRP 3.3 3.1 - - - +
111H LYS* 4.1 22.3 - - + +
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Residues in contact with ALA 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H LEU* 3.7 36.8 - - + -
67H GLN 3.4 15.3 - - - +
68H PHE* 3.9 6.7 - - + -
98H LYS* 1.3 77.2 - - - +
100H PRO* 1.3 66.2 - - - +
101H MET* 4.1 2.8 + - - +
108H VAL 4.2 0.2 - - - +
109H ILE* 3.6 2.8 - - - -
110H TRP* 2.8 43.5 + - + +
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Residues in contact with PRO 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G PRO* 3.9 3.3 - - + +
157G PRO* 3.7 14.4 - - + +
67H GLN* 3.3 11.4 + - + +
69H PHE 2.9 29.4 - - - +
71H ALA* 3.7 31.6 - - + +
85H TYR* 3.9 16.2 - - + +
98H LYS* 6.0 0.2 - - - -
99H ALA* 1.3 87.5 - - - +
101H MET* 1.3 67.4 + - - +
108H VAL 3.7 6.7 - - - +
109H ILE* 4.5 7.4 - - + -
128H ASP* 5.1 3.8 - - - +
131H ARG* 4.2 7.4 - - - +
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Residues in contact with MET 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G PRO* 4.0 6.5 - - - +
157G PRO* 3.4 20.9 - - + +
159G VAL* 3.3 34.5 - - + -
64H LEU* 3.3 29.8 - - + -
65H SER 5.1 2.2 - - - +
66H LEU* 4.1 24.0 - - - -
99H ALA 4.7 5.4 - - - +
100H PRO* 1.3 77.9 - - - +
102H ILE* 1.3 65.5 + - - +
103H LEU* 3.9 18.4 - - + -
108H VAL* 3.0 45.0 + - + +
110H TRP* 4.9 4.3 - - - -
125H LEU* 5.5 0.7 - - - -
131H ARG* 3.1 10.7 + - - +
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Residues in contact with ILE 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G SER* 5.9 0.7 - - - +
156G PRO* 4.8 4.3 - - + -
157G PRO 3.0 12.2 + - - +
158G GLN* 3.4 9.8 - - + +
159G VAL* 2.6 35.2 + - - +
2H PRO* 3.6 34.1 - - + -
3H ARG 3.4 26.7 - - - +
4H VAL* 3.9 11.4 - - + -
101H MET* 1.3 73.6 - - - +
103H LEU* 1.3 56.3 + - - +
105H GLY* 3.8 6.3 - - - +
106H VAL 3.6 21.3 - - - +
107H CYS* 4.0 2.5 - - - -
131H ARG* 3.6 18.2 - - - +
135H GLU* 3.8 17.3 - - - +
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Residues in contact with LEU 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G VAL* 3.5 31.4 - - + +
161G THR* 4.5 4.7 - - + -
17H PHE* 3.7 27.4 - - + -
18H PHE* 3.4 14.5 - - + -
21H LEU* 5.2 0.7 - - + -
64H LEU* 4.6 7.6 - - + -
101H MET* 3.8 21.6 - - + -
102H ILE* 1.3 71.0 - - - +
104H ASN* 1.3 83.5 + - - +
105H GLY 3.1 1.1 - - - -
106H VAL 2.9 19.4 + - - +
108H VAL* 4.0 11.4 - - + -
125H LEU* 3.6 35.0 - - + -
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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